Yes, you can use Morph Manager 4 to delete all the morphs at once, but there is a trick that you need to know. Before you load the cr2 that you are going to process into MM4, first you need to load a pz2, any pz2. Loading a pz2 forces MM4 to display a new button named "More Options". Now load the cr2 into the same window as you loaded the pz2 into, click the "More Options" button, and select "Delete all morph targets from file".

The above will delete all the targetGeom (morph) channels from the cr2, but it won't delete the valueParm (FBM) channels. You will need to go into the BODY actor and delete the valueParm channels manually.