Unfortunately, Sam can't quite abide a standard prison option herself right now. The spy's lesson was a real one, that they could turn around and cause still more damage, so she's sort of trying for what she deems to be the crueller option in theory, and one that keeps him under thumb and control, rather than risk him dying forever and a near-identical version from a near-identical world showing up and starting it all over again.

^_^ but yeah, I can see how he'd feel that. Everyone's got their perspectives.