The data path is not fully separate. You can download a new flight plan via Acars and you can load it into the FMGC. The FMGC does control pitch, roll, thrust, nav displays, navaid tunning and assumed location, aircraft position, etc etc etc. Putting that to the side both the database and the basic FMGC software is routinely updated, any one of those updates can introduce malicious code with expanded functionality. As proven by the way the CIA managed to blow up Iranian centrifuges. The last line of defence is indeed the crew, provided the system is designed to allow the crew the final decision.