Again, I'd say it is debatable whether Stonum's senior status should matter or not. There was a lot of discussion about Blount's year-long suspension because people said it effectively ended his shot at the pros (and he did in fact go undrafted despite his obvious ability to play at the pro level - though he did get picked up as an UFA), which is a much harsher punishment than the year-long suspension was intended to be.
And it's not about the university "owing" him something. It's about taking into account the unintended consequences of the punishment. If the punishment is meant to end his playing career forever, then that's what it is, but I doubt that would be the intent.
It sounds like I'm arguing that Stonum should be let off easy because he's a senior, but I'm mostly playing devil's advocate. I think his lack of follow-through on his probation is pretty damning, that he doesn't seem to really care or take the situation seriously.
Moralizing aside, I love Stonum, and I really hope this gets resolved in a way that includes both him being punished but still seeing the field (for totally selfish "I just want to see him to play" reasons).