I would say that your instincts are screaming at you, that this is not your miss right.
I totally understand where you are coming from, you are not a jerk, we can't decide on our feelings, but we have to listen to our instincts.
The fact that you do not see you both together in the future, is because she is not the right lady for you. This doesn't make her a bad girlfriend, or you a bad boyfreind, it is just that you know you don't feel the feelings you obviously know you should.
Please don't stay with her just because she has been through so much for you, that is like saying you feel obligated to stay, and that you would feel guilty to leave. By doing that you would be doing both of you a disservice.
You are obviously a kind person, and worry about her feelings, I think if you are totally honest to her about how you feel would be best for both of you. Afterall, you don't want to feel like this further down the line when maybe kids may be involved.
Don't feel bad, afterall dating is about finding the right person, you have dated and have decided that she is not the right person for your future.