Ex-theists are often like ex-smokers, sanctimonious and insufferable.

[Pyrrho]

Of course the good deeds done due to religion count.  Now, tell me, how many good deeds does it take to balance against a beheading?  

Edited to add:

When smokers and drinkers start beheading others due to their smoking and drinking, then we can start to talk about how such things compare with religion.  But otherwise, it is a bullshit analogy.

Were you a smoker?

I do not see the relevance of the question.  But the answer is "no."

But the problem with balancing the good with the bad the way you're doing it is you are holding each and every religious person responsible for the actions of every other religious person, living and dead.  ...

I am not doing that.  Please reread my posts, and see if you can find me stating such a thing.

Each person should be held responsible for their own actions.  In some cases, they only have a small part to play in a story, but their small part should be acknowledged.  For good or ill.