and I know it's not, but bear with me, they'll make you sit out a year but give you an extra year of eligibility.
The idea behind the graduate transfer rule is that a lot of players redshirt, which means that they can graduate in 4 years and still have one year of eligibility left after graduation. The rule allows you to transfer and use that year of eligibility immediately if you are pursuing graduate work in something your school doesn't offer.
The idea behind it is good, because if you really are a student just after an education and you want to do something in grad school that your school doesn't offer, without the rule you'd either have to forfeit your last year of eligibility or choose to wait a year before grad school, or just not go at all. However, the rule ends up being used for players just looking to transfer, like the guy that left Utah with Urban Meyer to go to Florida.
If they want to close the loophole and make it about the education, then give the guy an extra year of eligibility and force them to still sit out the first year. That way, they get two years of grad school paid for, which is how long most grad school programs take anyway, but it still allows a player to use that final year of eligibility after sitting out as a transfer.
I don't know that you'll see that happen, but that's the answer. Masoli's situation is unusual because he was kicked off his other team and was eligible for the grad school transfer rule. That type of situation is not likely to come up very often, if ever. I do agree that the NCAA should likely avoid trying to legislate discipline choices for schools/players. That's a Pandora's Box they don't need to open.