Tom was taken out form being Consigliere for a few reasons.

1. Things were going to get rough, don't want him being hurt.
2. He isn't a war time Consigliere, sure he can fight a war but if you want to use the skills of tom Hagen efficiently send him to do the legit family business.
3. When your planning something like they were the less people who know the better. Even someone they trust like tom. Although he figured it all out anyway because although he wasn't a Sicilian Vito had made him one.
4. I always thought a part of it was, tom was with the don when he made the peace so in a way tom was a party to the peace.

Michael did have complete trust and confidence in tom Hagen, you can see when the don has died and they are about to go to war he makes tom hang around. Pretty much reinstalling as Consigliere.