Luna - Not all followers of Islam disrespect women, gays, apostates, Jews, atheists and pretty much anyone outside that ideology. If you support freedom, then you support the right to religious freedom. The right to religious freedom has to apply to all, Muslims, Jews, Christians, everyone else. I think supporting that is important. The right to religion freedom must coexist with the other rights we enjoy and should not restrict them, but sometimes it does raise challenges which are not limited to Muslims. I have heard a number of times when orthodox Jews have refused to sit next to women on planes, for example.
This is a conflation of individuals with ideology. Not all Jews, Muslims or Christians disrespect women, gays and apostates but the ideologies do. Thus, the individuals following these belief systems need to practise, at an individual level, lots of cognitive dissonance to get from the point of 'apostates should be killed' to 'apostates should not be killed'. The subsequent behaviour then begins to be subject to individual whims - an individual's discretion to either behave in the prescribed manner, or not. It's clearly wrong to suggest that religious doctrines do not variously advocate all of the things that you mention. They do. If we accept this, then we do not have to tie ourselves up in knots trying to justify atrocities alongside 'but what about freedom to believe'. The solution becomes a simple one - change, amend or delete altogether those aspects of the belief system which are bad - and we do all agree that advocating marginalisation or worse of women, apostates, gays etc. is wrong, don't we?