Or say you have 80 very-part-time contributors who together match the output of 1 full-time employee, github is going to charge you as much as they would for 80 full-time employees.
Any pricing structure is going to have some people who get a great deal and other people who get screwed, but it sucks when you've selected a platform, invested in getting set up on it, and then have the pricing rug pulled out from under you.
I see two possible solutions that don't force you to switch vendors:
1. Have non-employees fork & submit pull requests. 2. Split your private stuff off to a different org & formally separate free stuff from proprietary, make the free stuff community managed.
If these are problems, I'd maintain that this is a "have your cake and eat it to" problem, on the one hand keeping ownership & control of the project and reaping the attendant benefit to the edx brand, and on the other hand getting people to hack on your stuff for free. But in any event this is a broader existential issue that exists across the OSS world right now (see express.js), so I'm probably reading too much into your case. :)
"These users do not fill a seat:
Outside collaborators with access to only public repositories"
So you have volunteers, working on your proprietary, private software for free. The labor is free & now you're complaining that you'll have to pay a per-free-laborer fee for the infrastructure to manage all these free-laborers? I hope I'm missing something here...