The mod works great, except that even when disabling "Can Corpse Check" in the CS, and giving them a class strong in Hand to Hand, they still loot corpses or run from a fight looking for a corpse with a weapon.

Has anyone found a way to stop/disable this?

Have you tried sneaking and "activate" to access the quick menu to change their behavior? I believe there is also a mod that facilitates access to those menus via some other method. I do not use CM partners...for the partners, so I cannot tell you, but there are some companion control-type mods out there that work with CM Partners...