I'm interested in what you mean by 'advocating mistreatment'. There's a gargantuan difference between 'disapproval' and 'advocating mistreatment'.
I completely agree with civil marriages for consenting adults, but would you say that churches should be forced to marry same-sex couples or to change their stances on homosexuality? That would be rather illiberal, wouldn't it? Whether you consider homophobia to be ridiculous and prejudiced or not, shouldn't people be entitled to their own opinions? To be accepted in a church for example is not a civil liberty - as an atheist, I certainly wouldn't expect or want to be married in a Catholic Church. Why should it be different for homosexuals, who are quite clearly condemned in that religious sect?
Well, granted, I don't think any respectable church is out there telling people to go beat up gays (er, except the Westboro Baptist Church but I did say respectable) but the thing is, religion-based reasoning is the basis for most homophobic arguments that often deny people their rights. The Catholic Church has gone on a crusade to discourage gay marriage. Within their own church - as you say - they have every right in the world to voice their opinion and to not allow it if they so choose. But it doesn't really stop there, does it - the rhetoric is everywhere.
It's not just, say, Catholicism with homosexuality, though is it? I personally feel that aspects of certain types of Islam are pretty harsh on women. So, yes, these religions and their followers have every right to their opinions but I just feel as if, what happens when these doctrines become entangled in the fight against people's rights and liberties? :/ Must I respect your argument on religious grounds, even if it is blatantly bigoted and if you had your way, it would lead to gross unfairness?