I'm so sorry this happened! I know that the Boy Scouts have been very problematic with LGBTQ issues, though they seem to have mostly gotten over that. But this sort of enforced theism is really troubling. I would not have expected a scout leader to say something like he told your son, and I think if you went up the chain to higher leadership, you would probably get some satisfaction.

I can't imagine that's got leader praying and making children pray falls within acceptable Scouting practices.

But I don't know. It's probably worth pursuing, though, if for nothing else than to fight for justice.