My Castle headcanon1 has always been that, when they finally catch up with Mal (oh, and they definitely do catch up with him; the idea that no faction within the Alliance would seek revenge for what he’s done is laughable) they decide that they can, in fact, “make people better”, and he is no exception. After the service he has done in exposing the corruption and cover-ups behind Miranda, they can’t just dispose of him, so they want to rehabilitate him and make him a productive, contributing member of alliance society.
They can’t simply re-format his brain directly, of course. It wouldn’t be compatible with his personality, and his underlying connectome would simply reject the overlaid neural matrix; it would degrade over time, and he would have to return for treatments far too regularly for it to be practical.
The most fitting neural re-programming they can give him, of course, would be to have him gradually acclimate to becoming a lawman. So “Richard Castle” begins as an anti-authoritarian man-child and acquiesces, bit by bit, to the necessity of becoming an agent of the enforcement of order.
My favorite thing about the current season is that, while it is already obvious that my interpretation is correct, this season has given Mal a glimmer of hope. Clearly the reprogramming isn’t working, and aspects of his real life are coming through.