IMO it just looks bad for EPFL if they decided to cancel the lecture based solely on this. If they knew about it, then why tell RMS he could hold a lecture only for them to cancel it on the last minute to bring back this topic again?
Exaggerating a bit but this is like inviting Linus Torvalds for a lecture, then cancelling it at the last minute because of his previous attitude towards the Linux git repository.
EDIT: I just read their response and they are boldly assuming that RMS would divert the topic from free software and open source during his lecture, which I find it very difficult to do so, unless asked, given what I know of his persona.