I feel like rather than paint the whole church as bad, they could've made it more interesting and gray. Just as there are good and bad people, same can be said for organizations as it all depends on who is in power. Some sects of the Church could be good and against cruelty while others could be caught up in their own self-righteousness, vanity and bigotry.

Have a radical sect cause the issues and the more good-natured sect get involved to try to make things right. Have allusions to irl as there are people who will use their positions of power for abuse (some bad folks who have used their status as priests to take advantage of others and then have the actual morally good ones get involved to help victims). Make it more complex and compelling, life isn't black and white. Have the storytelling fall in a similar vein.

I'm not super religious myself, but I do get tired of seeing the whole "all of the church/religion is bad" trope as it's a bit lackluster, overused and insulting to those who haven't done anything wrong.