I'm a Christian and I have no problem with Dream Theater.
I will say that because I am sensitive to certain content, I usually do pay attention to lyrics. As such, I tend to avoid hair metal in part because I'm not really interested in songs that are just about sex. I avoid death metal because I don't like music about harming innocent people. And so on.
Part of the reason I was drawn to most metal in the first place was because, even if there was criticism of Christianity, it was handled a bit more intelligently than popular music. When bands like Disturbed have songs with ridiculous lyrics like "Liberate your mind, you motherfucker" repeated 50 times over, Dream Theater is not only inoffensive, but refreshingly smart. I would feel comfortable talking about them in any Christian setting. Surprisingly, that also goes for a number of metal bands called "Satanic"--Black Sabbath, Iron Maiden, etc. all have surprisingly clean lyrics for the most part.
So no conflict here. Scenes from a Memory is a story, and a good one at that. Christian writers like Tolkein and Lewis were not in the least bit afraid to invoke pagan imagery in their stories, so I don't see why a bunch of musicians should be afraid to use a fairly common trope in their little rock opera.
Plus, if I had a problem with reincarnation, I wouldn't watch anime or play Japanese video games. They seem to use it a hell of a lot. I might be able to live without Dream Theater, but my life would lose some degree of meaning without Zelda games.