Encryption is not the end-all solution to security problems, especially if it's widely used and uncontrolled. Encrypting a protocol may solve one security problem but it can also create other problems. Like any other technology, it can easily be abused.
Bowulf has a piece on the use of SSL and the problems it creates with monitoring and content control.
Things will only get worse as virus writers and hackers adapt the use of encryption for network traffic, not to mention those users in your network who are knowledgeable enough to set up encrypted channels to avoid your security policy.