UrsusArctos: Shinji may not be thinking rationally here, but if Gendo had any sense, he would have convinced Shinji to disable the Eva and extract the pilot inside. But Gendo being Gendo fails at that.
Dr. Nick: The team strategy should have been obvious from the start: two Evas pin the zombie unit down, whilst the third rips the entry plug out, after which all that is hopefully needed is a quick shank to the core.