Hmm... I'm walking a fine line here. On the one hand, you asked for input from atheists, and I seem to be the board's most outspoken atheist so I figure I should rspond. On the other hand, pretty much anything I say is going to be taken as an insult by some here and will no doubt spurn them to angry posts etc.... but here goes...
Now, Your friend seems to be pointing at the Old Testament Bible (since he's addressing a Christian) and how the Hebrew God commanded them to slaughter their neighbours, stone each other to death, and do all sorts of other nasty things. It is hard for me to view such a God as anything but a monster. There is also no ban on slavery in the bible, and what it says about homosexuality and how to treat women is pretty horrible. A lot of horrible things have been done in the name of Abrahamic religions, but I think this is as much a reflection of the times and prevailing cultures, as of the religions themselves.
But if he's judging modern Christians by the Crusades, Inquisition, witch trials, or old testament he's really being a bit unfair. Very few Christians would follow that stuff literally today. The modern renditions of Christianity is a lot more serene and positive. The bible, and other holy books as well, are reflections of the times, and the prevailing views on morality of those times. We have come a long way since then.
Wars and destruction that some anti-religious people may try to pin on religion, are rarely actually caused by religion, nor were they even back then. There is pretty much always a more base reason, like land or power or money, etc. Religion in these wars simply acts as a catalyst or an excuse. It is easier to get your people to do horrible things you want them to do if you can get them obeying in an authoritarian way and if you can demonize (sometimes literally) your enemies.
As I see it, the most dangerous thing about the Abrahamic religions is its potential to get people to subdue their sense of morality and replace it with an obedience to authority, what they believe is "God". The bible story of Abraham prepared to kill his son for God is a good example. And there are many other scattered throughout that text, and throughout real life history.
The concern is that people may be convinced to do things they would otherwise hesitate to do, such as killing their children, blowing themselves up, drinking poisoned coolaid, etc, and they may even do it with great pride, if they somehow come to think God wants it. I think that kind of complete farming out of one's moral compass to religion, or other dangerous ideologies (it isn't just religion that can do this), is pretty rare though.
My other main concern, specifically with the Christian religion (and the Christ concept), is vicarious redemption; the sacrifice of Jesus. First we are told that we are so horrible, simply for being born, that we rightly deserve to suffer eternally in hell, and then we are told that we can escape this just punishment if we will accept and endorse the suffering of an innocent person, Jesus, as payment for what we have done. I find that incredibly disturbing. We would not let a killer on death row walk free because somebody else volunteered to be punished in his place. You should not be absolved of responsibility for your actions simply by agreeing to pass your personal accountability to somebody else. You do the crime, YOU do the time, etc.
So, I have some core issues with Abrahamic religion. But really, the typical Christian, Muslim, or Jew I meet in every day life doesn't cause me much concern. They are usually harmless and often very nice people.