I don't believe there is a way to change the name/location of the media folder within mojoPortal, but depending on your web site hosting situation, you may be able to do this by first moving the existing media folder to your desired name/location, then recreating \Data]Sites\[site#]\media as an NTFS directory junction point. That would make the media folder act as an "alias" that transparently links to your desired folder name/location.
As always, back up early and often before experimenting!
I hope that helps,
Jamie