From what I understand there really wasn't that much that would have been different had Tom been in the movie. the George Hamilton character just replaced the character. The Godfather companion talks about this.

Also in the commentary on the DVD, Coppola notes that had Hagen been in the role of the lawyer it would have been better because it would have shown how far that character had come that he was dealing with the vatican. he didn't say anything in the commentary about any changes that would have been made had he stayed on and probably would have mentioned this had the original script called for a Micheal vs. Tom storyline.

Keep in mind he was pretty much negotiating with Duvall up until close to the filming began so I don't think there was that much change made, probably just small rewrites here and there and obviously a lessening of the BJ Harrison role.

Duvall, on David Letterman pointed out that he wanted to make at least half of what Al was making for the film but instead they were offering 1/5th. I think it takes away from the film him not being there, but overall it's not that much worse than it would have been because the overall story would have been the same.