You can allow Skype in order to be able to utilize Skype while blocking P2P protocols. This will allow you to use Skype without allowing other harmful P2P protocols that are used by students to attempt to bypass the filter or that are used in peer sharing that can spread malware.
Over the summer, Microsoft released an update to Skype that makes it so that it does not require P2P protocols to operate. This means that schools can continue to protect their networks with P2P blocking while allowing Skype.
Make sure that you are running the latest version of the Web Filter and Skype clients. Also, ensure that the following domains are allowed: