Yeah good point, makes me think of Watchmen when Rorschach says to Dr Manhattan 'you could have stopped this' and Dr says 'I can change almost anything, I can't change human nature'
Dr. Manhattan and his lame excuses.
I think there's a subtle way his actions are explained. Dr. Manhattan sees his whole life outside the normal flow of time. He's removed from time in a way, and sees his life in a single moment. Every decision and action he will ever make or do, he knows at every point during his life, from point he becomes Dr. Mahattan. This foreknowledge puts him in a position of knowing but being unable to change what is meant to be.
Trying to skirt around religion here, but it kind of plays of the theory that if capital G God knows everything that has happened or will happen, then we really don't have freewill (lets not spiral into a debate about what is freewill, etc.) to choose otherwise. We would be living in a deterministic universe where everything is predetermined to unfold in a certain way, so even though Dr. Manhattan could do something, he is predetermined to do nothing.