Here is SJSU's three-point rationale:
1. Skype's End-User License Agreement [EULA] requires the user to grant use of university network bandwidth by Skype users otherwise unaffiliated with the university, and end users are not authorized to enter into this type of agreement on behalf of the university (i.e., the owner of the resource).
2. The operation of Skype's relay function is not in compliance with university policy because: a. It provides service to third-party people other than those conducting university business. b. It exceeds incidental personal use.
3. Skype persistently alters host firewall settings and increases the probability the computer will be compromised.
The preceding describes pretty much every peer-to-peer app extant, so we may be about to see some major sea-changes.