Turning the abilities off is one way... But after trying that and running a dynasty, the abilities were again automatically enabled in the next season. And I could only change the superstars that were on my roster.
I noticed that for PS2, the online update gave the FSS ability to people who didn't have the required ratings. Maybe there's an opposite to this. Is there some way to permanently get rid of the FSS feature? Maybe setting certain values in the database or something?