Priscilla beat the crap out of Superman in the BaTB cartoon, through a combo of magic and scheming. If they just did more of that consistently, people wouldn't have trouble buying her as both a physical and scheming threat.
Which is what they should be doing. Don't remove her as a physical threat, just have her be more clever and cautious on when she picks her battles. Have her concoct schemes that indirectly wear Diana down before going in for the direct fight. Also, don't rely just on the Cheetah powers. She's an archaeologist/treasure hunter in the DCU. It's not the characters fault writers forget her background