Assuming Worf left his Ambassador's position and returned to Starfleet, I think he would have gotten a command that fell under Admiral Ross. Bill had gotten many chances to work indirectly with Worf through Martok and Sisko and would be the logical Admiral to look past Worf's "official" record and give him a chance. Worf would have some powerful advocates as well: Martok, Picard, Kira and Riker would all have influence if they spoke up for him.
Also, remember Starfleet was depleted during the Dominion War. That's part of the reason why Nog got promoted twice so early in his career. The fleet would be getting rebuilt and experienced senior officers would be needed. I think Worf would definitely get a ship of his own.
As for the Enterprise E, I would bet on Captain Shelby. She had seniority over Riker, since she jumped past him in rank and got her own ship before he did. And she worked with the Enterprise crew to help save Picard's life and beat back one of the Borg attacks.