NCAA Football can not represent any current NCAA player. Reggie Bush is a former player and he can be represented, as proven when he was on the cover of NCAA 07. Really that situation doesn't matter. What matter's is that USC broke the rules, and now they have to pay the consequences. This isn't really that big of a deal and isn't a game breaker, I'd just think it'd make the game a bit more realistic.
I'm not even going to get into how bad Auburn deserves to be punished.