I know that from reading some of the other threads on the Michael/Tom relationship is mostly about his blaming Tom for Sonny's death and such.
But I think there are different reasons. More prominent ones.
When I watch the movie and see Sonny and Tom interact in front of Michael. There is a issue there, one of a certain level of disrespect(for lack of a better word).
Tom and Sonny interact in such a way that Tom is yelling at Sonny. Atleast one time I can remember in front of Michael. I dont think Michael wanted any part of that and stripped Tom. "No chance" of (that disrespect) that happening

You cant have your Consigliere yelling at the Godfather especially in front of your underlings.