Will changing an Apple ID remove the media content currently on the phone (iTunes?)
The good news is that iOS allows you to have a separate iMessage Apple ID then your iTunes store Apple ID. To remedy your problem follow the steps below:


Open Settings.app (on your son's device) and go to "Messages".
Scroll and tap on "Send &amp; Receive"
At the top select "Use your Apple ID for iMessage".
Tap "Create new Apple ID".
Enter in the information and follow the prompts.


After this is done, you can go to Settings.app -> iTunes &amp; App Stores, and make sure the Apple ID there is set to your Apple ID.

And, to firmly answer your question: No, having a separate Apple ID for iMessage and iTunes (and the process of changing it) will not erase content.

Note: instructions provided work best with iOS 6, but should be workable with iOS 5.