"Yes, it is clear why religions do not wish to alter scripture - but at the same time, that doesn't change that they must make a choice between doing so, or being complicit in the misuse of their scripture."

I can't agree. You're imputing guilt for misuse by some into the entire theistic population. If you accuse me of being complict because I refuse to alter what I consider to be the Dictated Word of God, then I'd have no choice but to tell you to bugger off and mind your own business.

" all religions, in particular the Abrahamic ones, are notoriously intolerant of being questioned or criticised."

Depends. If you criticize those people adhereing to a "minority" interpretation of a Scripture, you'll have a lot of cooperation from within the religion. No shortage of Christians who believe, for example, that Joel Osteen teaches a heretical version of Christianity. However, if you attack what is considered to be essentially a settled part of a religion's beliefs, then yes, you'll encounter resistance. That's not "intolerance" but a firm committment to what is believed to be the Recieved Word.

And yes, Religions are not democracies. If a religion is a democracy, it's no longer a religion.

"but that is not really a criticism of Islam (it's more just geographical luck)

Precisely correct. Islam is 1400 years old. When Christianity was 1400 years old, it was practiced in theistic countries by theistic rulers and their resistance to any sort of "libertarian view" was much the same.

"....often involves more fear of reprisal from fellow believers than government agencies, forcing such people to be in hiding and so on. The laws in question are part of the reason for that."

At this point, in almost all Muslim countries, the fear of social ostracization outweighs the fear of criminal prosecution. The Sharia courts seem happy to all apostates to be socially shunned and have difficulties with employment, the combination of which generally leads apostates to emigrate (and, from the Court's perspective, become somebody else's problem.)

"It is definitely plausible to say that society's laws poison religion in some manner, but looking at the history of religion, I would say that religion has never needed any help to poison itself. "

Well, that's because you have an entirely secular world view. If you have a wholly CHristian or Muslim world view, the your life has one purpose and one purpose alone, and that's to achieve the Next Life. The moment you take on that perspective, most of what secularists beleive is important, and the debates over what is important, becomes not so important at all.