Have you tried committing genocide to make sure you're not in the matrix? ... This is not the matrixes way to end you as you know too much. Trust me completely, you know what must be done.
Trying to change is good but you can't just ignore the past. His nightmares are ultimately self-made and whether he has them for the rest of his life or not ultimately depends on him. I believe they are well deserved for the things he did.