Remove tax exempt status for any "church/mosque/temple/etc." that preaches hate or produces nut jobs (including homophobia etc.), not the entire religion but one building at a time. Hit them in the pocketbooks and there may be a motivation to change. This should include all religions, for example Franklin Graham, West Borough Baptist, any mosque preaching hate, Catholic Church stuck in the dark ages..... Blow up a crowd, your mosque loses tax exempt status. Shoot a guy in a driveway for wearing a turban, your church loses tax exempt status...
This is not interfering with the right to practice their religion, still can worship sky fairies, not interfering with freedom of speech. If you are backwards and you hate, you just don't get the tax breaks. Apply it evenly across the board.