It was Michael who wanted Tom out because he wasn't a wartime consigliere. Interestingly when Michael tells Kay about Tom for the first time he tells her that he thinks he's in line to be consigliere, and explains what that means. Even then he tempers his enthusiasm by saying he's a "good lawyer" ..... not a Sicilian. IMHO there's a difference between someone who is a "good lawyer" and a consigliere in Michael's mind.

Vito never moved Tom out. He had turned the family business over to Michael when Tom was pushed aside as consigliere. Vito even consoled Tom, telling him, "I never thought you were a bad consigliere, I thought Santino was a bad Don, rest in peace."