I have a friend who lives at Stanford, where his mother is a professor. After he torrented some legitimate software (but used a Pirate Bay tracker), he was contacted by Stanford authorities. That was the first warning he received, he did not try to appeal the decision or break it again.
Stanford gives out automated warnings if you have a lot of torrent-y network activity (I got a few back in the day after downloading some linux distros), but as I recall they are only to notify students that if they are pirating music/movies/etc, they will be held accountable if someone from the RIAA or some other group contacts Stanford about it. If you're downloading legitimate software you shouldn't have anything to worry about (except for some occasional automated spam)
I'm not sure what my uni's stance on torrenting is, but it definitely has not stopped me from downloading over 1TB of... "legitimately vague" content http://i.imgur.com/oQE4J.png