Greetings Sojourn,
Lengthy articles attempting to paint the "unacceptable" as acceptable only go to show how unacceptable they are.
Is that your excuse for not reading it? Let us look at the points made rather than the length.
Executing a woman or man for believing differently is unacceptable,
That isn't what we are talking about, or else there would be no non-Muslims in Muslim countries. Apostasy refers to someone willingly disbelieving after embracing Islam.
and it's not just outsiders like myself that feel this way but take a look at some of the posts by Muslims in this very thread. There is a remarkable shift away from the traditional Islamic ruling, suggesting that apostasy (i.e. change of belief) is not itself punishable by death but only if it is accompanied by an act of treason such as waging war.
If you want to look for traditional Islamic rulings and whether there is a shift away from them, you should look to what the body of Islamic scholars have said, not what lay Muslims say on forum threads.
Again, this is remarkable as even an outsider as myself is aware that the Four Schools of Sunni Islam teach that those who leave Islam by a change of belief are to be punished by death (If I am not mistaken the most lenient position was of some Hanafi jurists who stated such a person is to be imprisoned for life.)
To the best of my knowledge, the Hanafi jurists say only the female apostate is to be imprisoned until she accepts Islam; the male apostate is to be killed.
Now why do some Muslims find executing people for believing differently problematic?
Hmmm... what do you tell your Christian brethren who find the very core of your faith, the trinity, problematic?
I do not think it is a matter of emotion or subjective opinion. It stems from human dignity.
There can be no greater dignity than following divine guidance in its entirety, without distortion or rejection. The Qur'an warns of previous nations who subjected the revelation to their own whims and desires and as a result, went astray.
Humans are born with a conscience, a will, and reason. The truth is out there, God has made His case so to speak, but faith has to be an act of free will. There is no coercion in religion, as your Book states so clearly, but that goes both ways. If a person chooses to embrace or leave a religion, that is their free will, there can be no coercion. If it is illogical to say you can coerce a person to become Muslim, it is likewise illogical to say you can coerce them to stay Muslim. What is the value of person's faith if the only reason she is practicing is because she is being forced to? Is it not meaningless before God's eyes if the heart is not there to begin with?
Our conscience, will and reason should not precede God's wisdom and knowledge. We are His humble creation and recognise His authority in ordaining how we should live. If we claim to love Him, we must obey Him.
With regards to there being no coercion in religion, it's important to note that there are two different types of people: a person who has not embraced Islam and someone who apostatised from Islam. Both of them do not fall under the same category. In the verse you are referring to [2:256], the believers are ordered not to coerce anybody into accepting the fold of Islam. This verse is not speaking about apostasy.
But if one, of his own free will, chooses to believe and enters Islam by declaring the testification of faith, then he is bound by his declaration and all the disciplines of Islam become obligatory upon such a person. If one, after accepting Islam, does not pray, he will be compelled by Law to offer his prayers; or if he refuses to pay the zakah dues, he will be compelled by Law to fulfill his zakah dues; or if he refuses to distribute inheritance as prescribed by Shariah, he will be compelled by Law to do so; etc. Once the person of his own free will accepts Islam, he has no right to pick-and-choose the laws he wishes to follow, rather he will be compelled to follow all the obligatory dictates of Shariah by Law. Here one cannot say or bring forth the excuse
Let there be no compulsion in religion, nor would it be accepted. This command only applies to one who has not accepted Islam as his way of life.
A simple example may help to further explain the point. In today's age, one is not compelled to take citizenship of any nation (e.g. United States of America); but if one of his own free will chooses to take on and accept US citizenship, he cannot pick-and-choose which law he wishes to follow. If the law of the land states that he has to pay tax, he will be compelled to pay it whether he likes it or not; of if the law of the land states he has to be drafted in the army, he will be compelled to join the army; or if the law of the land states he has to pay half his wealth to his divorced wife, he will be compelled to do so; etc.
Let her leave, let her follow her conscience and reason, as she has a duty to do so.
What if their so-called conscience and reason takes them and those around them to Hell? The duty rests on others to try and prevent this from happening.
It is a move towards less freedom
Sometimes having less freedom is beneficial, as in the examples to prevent hate crimes. In some cases it can save a person's life, as in detaining a severely depressed person trying to kill themselves.
I agree that we can not turn a blind eye towards war crimes or harassment of people. But it does go to show that Christian and Secular nations provide a better standard of living even despite some of the cases you mention above. Millions of people are fleeing to Germany and not Saudi Arabia or ISIS held territory, and I don't think it's only due to economic reasons, but also do to the culture and freedom that is in Germany and other Western countries.
Rather than reduce the Islamic world to Saudi Arabia and 'ISIS held territory', you would do yourself more favours to remember how much western culture owes to Islam's rich tradition. Templar Historian, Tim Wallace-Murphy, writes in his book:
Even the brief study of history revealed in these pages demonstrates that European culture owes an immense and immeasurable debt to the world of Islam. Muslim scholars preserved and enhanced the learning of ancient Greece, laid the foundations for modern science, medicine, astronomy and navigation and inspired some of our greatest cultural achievements. If it were not for the inherent tolerance for the People of the Book that was manifest within the Islamic world for over fifteen centuries, it is highly doubtful that the Jewish people could have survived as a racial and religious entity, and we would have lost their contribution to art, medicine, science, literature and music which is almost beyond measure. We in the West owe a debt to the Muslim world that can never be fully repaid. Despite our common religious and spiritual roots, we have thanked them with centuries of mistrust, the brutality of the Crusades and an imperial takeover that was conducted with callous indifference to the needs of the peoples we exploited.
Tim Wallace-Murphy, What Islam Did for Us; p. 215
Christianity does not have an absolute version of civil laws that are meant for all places and all times that we are attempting to resurrect in the Modern Age. This means that laws can vary from time to time, and even between two nations during the same time period, it also means that there is movement towards creating a community ever more in line with Jesus' teachings, and if possible a society as well.
It is not only laws you are referring to, but doctrine as well. The fact that there is no way for Christians to ascertain Jesus’ actual teachings means that the Church has used ‘Sacred Tradition’ to extract out of the Bible whatever verses that might be construed to support their doctrines. Even a customary reading of the Bible does not lend itself to the numerous beliefs and practices of today. Thus, it is somewhat ironic for you to speak of Jesus’ teachings and in the same breath boast of modified laws.
A clear understanding of human dignity has been developing over time.
Well, the direction of where that dignity is going is debatable.
Referring to the Roman Emperor of the 4th century or a Pope's fallible opinion on a civil matter in the 12th century is a moot point.
Or perhaps inconvenient when you realise it wasn’t what you expected.
You're saying this dogmatically and it might make sense to someone who already believes, but as an outsider who does not follow Muhammad, it does nothing to make your position more believable or reasonable.
It is easy for an outsider to appreciate the preservation of the teachings of Islam and their comprehensiveness. Simply reading a biography of the Prophet :saws: will illustrate the numerous teachings from him in all spheres of life. The fact that this Law was revealed over a thousand years ago and yet is applicable today and provides the solutions for our problems, is evidence of originating from an All-Knowledgeable, All-Wise Legislator.
As GK Chesterton said, "The true soldier fights not because he hates what is in front of him, but because he loves what is behind him.” You mention St Augustine, the brilliant African Churchman and scholar of the 4th century, who lived in present date Algeria and whose Christian community has been all but whiped out. He lived in a time when the Roman Empire had converted to Christianity and it was being sacked by countless pagan tribes. The idea of Christians fighting in war was controversial because for centuries Christians had for the most part abstained from military duty and lived pacifistic life styles. But now the Empire was Christian and involved in a constant war and defense against the tribes of norther Europe, and Augustine had argued that the Empire did have a right to defend itself. His statements in his book The City of God would become the starting point for the concept of Just War:
I take it you will agree, then, that operating on the basis of love alone is an impractical worldview.
I can see that your motivation is good and that you hope and pray for non-muslims to come to Allah because you genuinely care for them. And that is truly beautiful. 
