I'd bypass it but I don't know if you need to plug the ends, Mike. Occasionally when the diaphragm goes bad mechanical pumps will start sucking oil in (from the inside of the engine), but if you don't see any coming out when you unhook it and run the engine, all the pump will do is suck air in and out. I ran oil filter lines through the opening where my mechanical pump used to be...
~ Jon 1952 1/2 ton with 1959 235 | T5 with 3.07 rear end