Choosing not to believe the hateful parts of any religion does not rehabilitate that religion. It's not out of line to say X religion sucks because a core tenet is tied to homophobia, patriarchy, or the like. The comment stands on its own merit even if people choose to ignore the nasty bits.
Many Christians are becoming more tolerant of homosexuality. Christianity still sucks because it holds to homophobic and patriarchal values. To take it even further, the church apparatus / organization enables pedophiles and encourages cultural imperialism. So Christianity sucks. How is that even a controversial statement?
If it becomes the predominant interpretation and effectively overrides the literal reading, it might as well be a rehabilitation in all but name.
That doesn't mean you cannot criticize the religion in its original form, so to speak, when those ugly statements are still present in the texts.
Nor does it mean any other structural problems can't be brought up. I wouldn't call that controversial either, nor am I asking to erase the historical dimension.
My point is that there is value in the more liberal and reformist sides of a religion and that can be a positive influence on the lives of vulnerable groups.