To try and answer your points in turn:
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. That is not a problem of current sensibilities - criticism of religion, and of God, predates the Abrahamic religions (Epicurus, for example). Criticism of the religions themselves has existed since they began - but all religions, in particular the Abrahamic ones, are notoriously intolerant of being questioned or criticised. Not all members of said religions, of course, but in general due to their "unquestioning loyalty to God" nature. This same problem of misuse can't be said to apply to non-religious things, because unlike religion secular laws do not demand unquestioning, undemocratic belief in a concept without any sort of logical or moral justification.
When it comes to the 'libertarian' position you speak of - yes, it certainly does exist, I agree. I would certainly argue it exists far less in Islam than other religions, but that is not really a criticism of Islam (it's more just geographical luck, in that the largely Christian western nations are on average more developed and more secular in their views on government policy as a result of that).
On your point about the enforcement of e.g. apostasy laws, yes - the point I was making was not so much that they are necessarily enforced, but rather that in those nations turning one's back on their religion or other blasphemy 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.
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. One can see this in the end of the Islamic Golden Age, Christianity's propagation throughout much of the world by force, and so on.
