Tolkien actually made a point of mentioning - in writing, on several different occasions - that LOTR was not in any way allegorical, and he seemed to be rather offended when people insisted it was.

I would be surprised if the bias v. religion from TGC makes it intact into the movie, and I think the rational will be a blend of, "Yes, we want people to bring their happy children to the theater and not wander off thinking distractedly that they really thought this was a childrens movie." and the fears that there will be back-lash from those ultra-religious activists. They do have power, as quite a lot of them hold some purse strings. It's not a mass conspiracy though - it's what the company looking to make money feels will be the safest choice for raking in large wads of cash. Movies that are more militantly gay/anti-religious/etc do not make as much money. Dogma rather proves that point brilliantly.