Hi root,
If you noticed, one of the conditions for the
hadd (those prescribed by Allah in the Shari'ah) punishment to be applied is that their must be
no doubt that someone has committed the crime, i.e. no other possibilities. As for any excessive or unjust suffering one endures, it either contributes to more reward for them, or it expitates some of their sins, for which they would have been punished.
peace.
EDIT
I'm going to add some of my other explanations here as well, on various Islamic punishments.
Apostasy:
http://www.islamicboard.com/20595-post1.html (Islam and Apostasy)
Fornication/Adultery/Rape:
http://www.islamicboard.com/130001-post19.html (What is the ruling on the crime of rape in Islam?) http://www.islamicboard.com/130000-post18.html (What is the ruling on the crime of rape in Islam?) 
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