There's no way he'd let Tom go. Tom knew too much about him. If Tom left his employ, the attorney/client privilege Michael enjoyed with Tom would disappear. FBI already had Tom listed in the Corleone Family org. chart we saw at the Senate hearing. After breaking with Michael, Tom then could have been subpoened and forced to tell all about Michael.
I don't think that's true.
It's my understanding that attorney-client privilege extends permanently, as long as the communication took place while there was an attorney-client relationship.
Also, it doesn't apply to criminal activities, so I don't know how much protection it really afforded Michael and Tom.
Still, it's hard to imagine Michael, at the height of his ruthlessness and paranoia, allowing Tom to go his own way.
