I'm doubtful. I believe you could easily spoof ADS-B and ACARS messages, but I'm not sure how that gives you control. The best I can think of is that you could spoof other airplanes nearby, and trigger TCAS (collision avoidance) to automatically move in the opposite direction. There is no way the pilot's would notice this, though.
The only other option is, as another commenter mentioned, a buffer overflow, or similar, that would allow the ACARS receiver to load a program in the FMS. In normal operation, FMS programs are not controllable remotely.
The only other option is, as another commenter mentioned, a buffer overflow, or similar, that would allow the ACARS receiver to load a program in the FMS. In normal operation, FMS programs are not controllable remotely.
This is the clear implication in the article - compromising the ACARS receiver, then using that access to further compromise another element like the FMS. The article states that the pilot can regain control by disconnecting the AP.
Note that maneuvers prompted by TCAS aren't automated. The TCAS system tells the pilot, who then obeys the machine. (Or sometimes he doesn't, and then the two planes might bump.) So, yes, definitely can't go unnoticed by the pilot, since he's an integral part of the system.
The only other option is, as another commenter mentioned, a buffer overflow, or similar, that would allow the ACARS receiver to load a program in the FMS. In normal operation, FMS programs are not controllable remotely.