Andy, an interesting novel but not really possible.
For a start, although the T7 is fly by wire, and as such controlled by computer systems, and the FMS cannot be changed without manual input. There is no evidence it can be "hacked" or the flight data altered remotely. Therefore one or both of the flight crew would have to be complicit in the scheme - no evidence at all.
The flight data can be loaded prior to boarding, BUT will be checked upon loading the FMS. Such details could/would not be overlooked by any flight crew. Such wild variations in waypoints and FL's would be like noticing you are putting with your driver.
The ACARS and transponder can only be turned off manually - so would need someone to physically to do this. Unless there is an electrical problem you would never turn off either - and for both systems to be turned off at the most opportune time is too big a coincidence.
If these "agents" were involved the E&E bay would have been the target and the flight crew would have immediately squawked this.
Entry into the cockpit is virtually impossible even if you have the code you have no chance of entry if the PIC denies entry.
I hope like hell that the FDR (unlikely the CVR will be of any use) is found soon to stop these crazy theories.
Sadly the outcome will not make a blockbuster novel or movie. At best it will be a jet catastrophic failure - like no other insofar as it flew another 7 hours, at worst (and most likely) it is another Egypt Air.