The Healy precedent cannot be read to state that universities are not entitled to de-recognize groups as long as they have "substantial justification." They ARE entitled to do so.
You can argue about what "substantial justification" is, but I don't believe that there has ever been a court case finding that a university withdrawing recognition from a fraternity that failed to meet university GPA standards (or the like) violated any Constitutional rights. Given that the Supreme Court recently stated that a university's stated educational goals are such a compelling government interest that they survive strict scrutiny (Grutter; Gratz); I'd be extremely surprised if there were any such case in the near future. Public universities are allowed to set all kinds of seemingly arbitrary standards for student conduct. (See the University of Virginia, which may expel you for lying to a fellow student:
http://www.virginia.edu/honor/intro/explain.html). Heck, it's pretty arbitrary that UF won't give you a degree in Psychology unless you pass Statistics. But it's strongly related to a legitimate educational goal, so it's perfectly constitutional, even though it impedes your freedom of thought. It would be quite simple for UF to explain why its educational goals are impeded by recognizing fraternities that persistently failed to meet these standards over multiple years.
At any rate, at best, the issuance of these policies doesn't give anyone any federal right to sue (I can't speak for every state); there wouldn't be a cognizable injury until the de-recognition occurred, or at least was imminent.
You can be certain that UF has an excellent legal team advising it on these matters. To me, the standards look carefully drawn to survive scrutiny.