This comes down to your allowance and interpretation on self-determination. There are consequences for every action - sometimes positive, sometimes negative. MIT made a calculation and rolled the dice. Most people are pleased, but it just as easily could have gone the other way. Every organization and individual has this right - you're essentially asking if its okay to make this choice if the outcome is negative - yes it is. Thats up to the individual to decide. Stallman made his choice and so did MIT
However, as a university it still seems like dangerous territory. I think communists are just as sickening, in light of the horrors of the twentieth century. Should I fire them if I'm making those decisions at MIT. Like if a professor said the gulags are a worthwhile evil on the road to socialist utopia? Is it really necessary to end a person's career when you disagree with them on matters unrelated to their work?