that sucks, sorry man. Been through something similiar myself a few years back, and it sucks. No way around that one. In my experience, at least, you're better off trying to make a clean break, at least for a while, rather than keep holding on. Just draws things out, and eventually it gets nasty, because while one side has been done with the relationship for a while, the other really hasn't let go, so there's a whole "second" breakup, and this time, the other side isn't as close to the issue, comes off as cruel, and you feel worse about it. Just my experience.
Another vote for the camp that feels that the religion aspect really wasn't that big a part of it. It's the reason she went with, but partially because it's something you couldn't refute, couldn't promise to change. (Mine was from Michigan, and said she couldn't see herself staying in New England, and didn't want to ask me to move. To show that that wasn't really the issue, she still lives in roughly the same area, 4 years later, so she wasn't in SUCH a big hurry to move, I guess).
In your case, sounds like some doubts, the strain of a long-distance relationship (religion aside, not having sex when you ARE together has to make a long-distance thing even tougher), and her getting ready to move and start another chapter in her life.
The bit with the dog is going to be tough. Makes sense that you get it, since she's continuing school, plus it's your favorite kind of dog, named after your childhood pet, etc. It's going to be tough with him around, though. One more thing to constantly remind you of the ex, and either depress you or make you less excited to see the dog, which isn't fair. Makes it tougher to move on from her, as well. Doesn't sound like she can take him, though, and not fair to the dog to get rid of him, so gotta do the best you can there, I guess.
Just as an aside (and not trying to wreck the thread at all, maybe it can spawn a different thread if it sidetracks too far?), but I don't understand your position on the religious debate, I don't think. You seemed to indicate that once someone is "saved", that they're saved no matter what, and that can't be revoked. Really? I would tend to think that even if you're a perfect Christian, take Jesus into your heart, etc, your salvation would still depend on what happens after. If a good, Saved person snaps after a tragedy and ends up sinning (say, killing another, or themselves, or whatnot), shouldn't that have an effect? If you can choose to walk into the light, can't you choose to leave? I would tend to think it could be revoked, otherwise your actions in life are meaningless. If you're a good child in Sunday School, get Confirmed, etc, then you should already be considered Saved at that point if you were to die, right? Plenty of those children later stray, however. Would think you could be "saved" again later if you come back and repent, but "once saved, always saved" doesn't make a whole lot of sense to me, from a logical standpoint...