He absolutely has the right to tell them what they should do. Presumably, MIT was making these educational materials available for the purpose of furthering the common good. Removing them does nothing to serve the common good, thus MIT is acting against its own goals (as we perceive them), which, logically speaking, is total bullshit.
It's a sound argument, and doesn't presuppose any special rights or privileges - merely the ability to analyze the purpose and effects of others' actions. Capacity for moral judgment + societal cost/benefit analysis + free speech rights = the right to tell others what they should do. We do this all the time: the US shouldn't invade Iraq, Microsoft shouldn't abuse its monopoly, the MPAA/RIAA shouldn't sue old ladies whose grandkid downloaded a song, that racist pastor shouldn't be racist, etc. etc. It's called advocacy.