Unfortunately, you cannot limit the use of Babylon plug-ins, but there is a way to get rid of the ones you need. Simply access the following path:
C:\Program Files\Adobe Reader XX.X\Reader\plug_ins\Babylon where XX.X is your version of Adobe Reader and then delete the files you don't need.
After Adobe Reader starts, go to its preferences and Enable protected mode at startup. This will also increase the functionality of Babylon and Adobe Reader.