Having been in this game for a long time, I have no reason to believe that there are no programming errors in the FMS (and the ACARS link to it) that would allow for either overwriting data that should not be overwritten, or arbitrary command execution.
I can't imagine a hack so sophisticated it would take control away from the pilots, but crashing the FMS or updating routes, that's entirely plausible.
It's happened to so many software system and so often that to believe the entirely unsecured ACARS system could not be vulnerable is naive to say the least.
How a simple programming error can lead to disaster:
Buffer overflow - Wikipedia, the free encyclopedia