iPhone Configuration Profiles - Creating / Modifying
The configuration profiles are normal XML files, you can modify them with any text editor. Also, there is an iPhone Configuration Utility to create new profiles. On the iPhone Support Enterprise site you can get more information about it. Just e-mail the modified config file to your device and install it.

I checked the mobileconfig from my last University and there seems to be no explicit setting to allow people to save their passwords, to I guess there is one to deny it.