The key here is the 6th Year Waiver....
Comparing Mbakwe to Stoud is useless, they are completely different scenarios. The Stoudemire situation was simple math, there was really no chance he wasn't getting a MRS.
On to Mbakwe....
Typically, the only players who are granted a 6th year are players who can explain that they missed significant amount of time because of either an injury or something completely outside of their control.
Kim Royston's situation was a bit peculiar that he got a 6th year. Before Kim was granted his, I thought it was doubtful. He missed his transfer year, which he used as a RS and then was injured in his 5th year, was granted a 6th. That was considered a surprising granting of a medical hardship waiver, because his transfer RS wasn't really outside of his control. I think there were some family issues (illness) which is why the NCAA granted the 6th year.
More similar to Mbakwe, Illinois had a QB named Beutjer a few years ago who was granted a 6th year.
He transferred from Iowa to Illinois following a fight with a teammate and he said it was best for him to leave, he was in trouble in iowa (etc.)
He then got hurt in his 5th season, and he was granted a 6th year.
Mbakwe's situation is going to down to how the NCAA looks at that one year he had to sit out:
Scenario #1: This is a kid who was in legal trouble, the coach didn't let him play because of that legal trouble to which he plead guilty. He missed the season because of his own bad behavior - - he doesn't get the 6th year
Scenario #2: This is a kid who was accused of a crime in which the prosecutor offered him a deal (that they likely wouldn't offer a guilty party), he was the victim of a false accusation, and it was outside of his hands - - he probably gets the 6th year