Basically, Colter has stolen another man's life, and the end of the movie gives no indication that he'll ever tell Christina what's going on -- how could he? She'd probably just assume he had a psychotic break. This "happy ending" is actually a terrible situation for everyone involved: Colter is walking around in the body of a man he knows nothing about, and Christina is now dating a complete stranger pretending to be Sean. There's a name for that, by the way, and it's called "rape by fraud."
"We don't have those laws in the future. Uh, I mean Minnesota. Where ... I come from."
Say Colter does the right thing and stops seeing Christina -- he still has to deal with the man's other friends and family and with his job as a teacher. Colter is a soldier, so unless he's also been getting a degree in education on the side, we're pretty sure that he's about to engage in some Kindergarten Cop-style hijinks. He's going to have to fake his way through basically every interaction he has with everyone, like the guy from Memento, but with fewer tattoos.
Our finest team of mathematicians were paid to whip an intern while he calculated the film's precise genetics.
Add this to the fact that, per the movie's ending, the Source Code (the machine that allows Colter to quantum-leap into Sean's body) was actually creating alternate timelines with every attempt to save the train. This means that, in theory, an infinite number of Jake Gyllenhaals will be creeping out an infinite number of Michelle Monaghans in an infinite number of universes, forever.