Upon reflection, I'm gonna go with a modified version of MaryCas' theory here.

Except for the incidental death of Geary's playmate, Michael never eliminated anyone who was not either a proven enemy or a potential danger.

Even if Tom had left the family and gone to work solo in Vegas, I don't think Michael would have taken any overt action against him.

I'd agree with what Olivant said above:

I don't think Tom would have been in mortal danger. However, he certainly would have been put out of Michael's life.