I think that even if Tom would have stayed with Mike,given Mike's paranoia and his need to be perceived as a ruthless leader,Tom's days were numbered.
When Tom asked Mike "Do you have to wipe everybody out?",or words to that effect,the die was cast. He should have kept it to himself. Not only was it disrespectful,but to say it in front of Rocco served only to embarrass Mike.
I'll bet that at some point,Tom,(overestimating his "value" to Mike),would have lost it and confronted Mike about a lot of his decisions,especially his murder of Fredo.

It's a shame Tom wasn't in III. What a great character arc we could have seen.