By inhabiting Sean Fentress' body by Colter Stevens in Source Code, hasn't the rest of his life become miserable in the altered timeline? Is this why Dr. Rutledge tells him (probably lie) they can't change the future?
There are two realities here. The Sean from the world where Stevens is a soldier is the first one. In this reality Sean has died in the train bombing.
Inside the source code, there is no Sean. Sean's conscience is replaced with Stevens'. The actual Sean dies in the train with no knowledge of a bomb. The other Seans are all Stevens' conscience trying to stop the bombing.
In the last attempt, Sean (Stevens' conscience) manages to stop the bombing. Ideally this world should terminate right after. However, this alternate reality is somehow real too. Stevens gets to live the remaining of his life as Sean in this.
Sean's life is not made miserable, but the ones who knew him would now find an altered version of Sean and will find it extremely difficult to deal with. However, those portions are not dealt with in the movie.