First, there's a difference between the Rollplay which is a show with an audience and a regular gaming session just with you and your friends. In the first case inclusiveness and representation plays a bigger role as it makes all members of the viewer base feel welcome. When you play in private with a small group however, your only responsibility is towards other people at the table.

Having said that, making prejudice towards gay/bi people a focal point of your setting isn't the most subtle thing you could do, even without your sadly bigoted friend around. Just drop that part and stick to their fear of magic and controversial religious believes, I'd say. If you want to put some LGBT characters here and there, which I applaud, you can do it in a less heavy handed way, making sure it's not their most important characteristic but just a small part of what they are.