Now the Egyptians are saying the plane was on course when it disappeared from radar, which contradicts the Greek ATC data.
http://www.bbc.com/news/world-middle-east-36365256
It's important to remember that the Egyptians have a strong motive to lie. If the regime can make the argument that this was terrorism (even if it wasn't), then they'll say that terrorist threats abound. This will be used to justify Sisi's crackdown on civil liberties, on the grounds that the world is too dangerous for people to have human rights.
We've already seen Egyptian dictators lie about plane crashes for political purposes. Remember EgyptAir 990, when the co-pilot committed murder/suicide by flying the plane into the sea? To this day, the Egyptians claim that the NTSB was wrong because no Egyptian would ever commit such an act.
https://en.wikipedia.org/wiki/EgyptAir_Flight_990