One alternative would be to make it free for "independent users" but fee-based for universities and other institutions around the world. One could in worst case maintain a large database of IP addresses to sieve out universities and (e.g.) companies from "independent users".
This is a trust based system and, of course, there would be scammers but I think most universities are honest and would pay the license fee. But then again, what stops ScamA Uni., ScamB Uni. and ScamC uni. from creating a VPN tunnel, splitting the fee and getting by the system that is used right now?