I suspect the Doctor of thinking that actually, the universe is a damn sight safer with River Song safely locked up; she has basically been trained from birth to be a psychopathic killer and I don't think her conversion to the Doctor's side has changed that (she was, after all, prepared to let everybody else in the universe die rather than live with the pain of knowing she'd killed the Doctor, which seems pretty psychopathic to me).

Of course, it may also be that she's safer in prison; the teenyweeny people may not be the only ones who think she deserves more than prison for killing the Doctor, after all.