Yes the rules are different. The SEC schools are generally inferior in their emphasis on education than the Big 10, ACC, Pac-10. Just check out the test scores.
This also applies to SEC graduation rates of their athletes in general.
So yes, a person who has a relatively clean record gets a lighter sentence than someone with a checkered past would get for the same crime.
It appears you are a USC fan (or at least a PAC-10 fan). Nobody who is objective is going to defend this unethical behavior by Reggie Bush and USC. Bush should be stripped of the Heisman, USC of its title, and the NCAA should place USC on sanctions.