I doubt they would ditch SatAM. SatAM is just too important to most Sonic fans of the cartoons. Plus Penders don't own any of the characters in SatAM given they're all before his era and they made it over to post-SGW. The only reason I can imagine Sega would be against SatAM in Prime would be eww, naked chipmunk!
Not from Penders, avoiding "lawsuit over Sonic like the one with Ken Penders before."
Someone from SatAM creative team could always just showed up and claim they're the one who creates the characters.
Remember how SEGA avoided releasing Sonic 3 after Michael Jackson died?
(Last ones, Steam version and NDS version, were released when he was still alive)
Michael Jackson would have no problem with SEGA releasing the game over and over again since they are always in good term.
The problem was after he died.
Whom the music that Michael created's right belongs to?
The Jackson estate lawyers or the six composers who worked for four weeks alongside Jackson (Brad Buxer, Bobby Brooks)?
Legal battle is tiring.
If they could avoid that, they would avoid that.