Late reply to an old thread, but before discovering the remove functionality, my split body then delete workaround to discard the unneeded portion has been to split the body, extrude the unwanted section through itself, creating a functionally nonexistent body, then combining the wanted and unwanted bodies. Since the unwanted body is invisible and can't be interacted with as it has no geometry, I haven't run into an issue where the invisible geometry causes an issue with the retained body, but combining them cleans up my bodies list.
I'm wondering if that couldn't be it's own function with that whole process running in the background, somewhat like the sketch trim function for bodies being split and discarded.