It would be ok to include a religious group, but we don't have to call them Mormons, as I posted previously. Using a fictiona name will likely minimize legal exposure.
If the company won't even use real names for the weapons in the game (FNFAL, HK G3, etc, which are trademarks, and therefore create substantial legal exposure) why does anyone think they would name a religious denomination?
Not to be a wise ass, but maybe because they aren't copyrighted?
Secondly, the FNFAL, HK G3 are all weapons that are designed after the divergence so they technically shouldn't exist in the fallout universe.
The church of the latterday saints or any religious group for that matter are founded before the Divergence and could just keep their original names.
I am not trying to offend you by what I am going to say, but in my opinion you are making it bigger than it is. Knowing Bethesda and Obsidian, they really arent going to try and demean it in any way. I am certain they will treat any religious group respectfully.
The problem is that there are always people that are going to be offended by it, and there is no way to stop that. As long as they keep the discussion open, and the content respectfull (as much as is possible in a world that is nuked into oblivion) there shouldn't be too much of a hassle.
Besides, it's a world wide release so the overall damage will be relatively small.