One thing I think that the guys working on the university should consider- historically the ghouls have been good guys, if self- interested. In otherwords, they usually have helped the main characters and thus have a good relationship with them (one of the reason Virgil is still with us) but they have their own interests to defend.
The ghouls have a pretty good sense of the shit storm that is gathering around them, and they probably would lean towards a third position- neither League nor Other, and thus, probably with us than against us. That said, they aren't the most trusting and they would be willing to sacrifice us for their own ends.