Hey Tom,
I see how this could be problematic. In general, Local SEOs will cite the guidelines Joey has, in which Google states they don't want this:
Location information, such as neighborhood, city, or street name, unless it is part of the real-world representation of the business.
So, short answer here is that you need to leave your name exactly as it appears in the real world on your websites and the citations that you can control (and, of course, your Google My Business listing). I wonder if it would be possible for you to reach out to the top 20 aggregators appearing for your core search and ask them to edit your listing name. If not, then the consolation here is that the playing field is level if competing colleges area all suffering the same fate with the aggregators. In other words, their percentage of NAP inconsistency would be the same as yours.
Anecdotally, what you're experiencing is also experienced by all multi-location businesses that list their locations on Facebook. Facebook won't let you have more than 1 FB Place with an identical name, so you have to be Joe's Diner Boston, Joe's Diner Chicago, Joe's Diner St. Paul, etc. Again, because their competitors are all in the same boat, it's something they don't really have to sweat.
100% NAP consistency isn't normally achievable. You want to be as consistent as you can, but don't stress about attaining absolute perfection, and my bet is that the inclusion of your city names on these aggregators is not hurting you very much, if at all. So, this would be a see-what-you-can-do-and-then-leave-it-at-that situation. Hope this helps! Interesting thread.