'Underneath all that intellect, you're the darkest of all of us...'

Although Harolds reasons for his actions were very clear, that doesn't mean he can't be the darkest one.

The fact that he created a God is already something very eery.

I think his speech in TDTWWA indicates that he lives alone not because he cannot be charming, we know that he can be charming, we have seen him seduce a woman in Hong Kong, but because he doesn't trust people. He was disguisted by the way society was going, the killing squads in Laos etc. he was hurt by being betrayed so many times by the goverment which murdered his friend, then by Dillinger. Building a machine that can uncover anybody's secrets probably just added to his paranoya. If you remember, the only reason why talked to Grace was because the Machine kept pointing him to the only person in the park that didn't keep any secrerts. And Grace also had mayor trust issues steming from living with her alcoholic father. So Harold isn't Sheldon Cooper from The Big Bang Theory, he has good people skills just not good enough to predict if someone is a traitor or an assassin.

Actually, the lack of people skills annoyed me more in Reese and Shaw. They are elite spies. They may not be the most warm and fuzzy but they should at least be able to pretend to be friendly. James Bond is probably a more realistic portayal of a spy, somebody who can charm and seduce anybody, use them, kill them and walk away like nothing happen. And if James Bond is more realistic, your show is in trouble.