Michael Corleone considered Tom Hagen equal as a brother and he was the only one he turned to, when the whole family was put on suspicion. Mike never would kill Tom Hagen, as Hagen protectd Mike's family from harm. They had their arugments, but the love of brothers was there. He never considered Hagen not to be a friend or brother, unlike what he did with Fredo. He always thought highly of Hagen unlike Fredo.