There's a very simple way: delete iTunes. XD XD
(On a more serious note, no, don't actually delete it, seeing as it's an app that comes with Mac OS.)
No, I don't think there's a way to stop certain apps from reacting to the media keys.
Yeah, I myself sometimes wished there were a way, particularly when I'm using both Cog and QuickTime Player.
However, you can use Cog's Hot Keys instead of the keyboard's media keys.
The Hot Keys will work while focused on any program, just like the media keys, but unlike the media keys, it only controls Cog.
You can set the Hot Keys in Cog's Preferences.