The aircraft was probably taken to 45,000 feet and the engines possibly turned off, to deprive the passengers of oxygen.. I believe the cabin pressurization is enabled by the engines, so killing the engines temporarily would depressurize the cabin, killing the passengers. Then the aircraft glides, engines restarted, passengers are now dead then aircraft can be taken to covert location and landed.
And you know all that how?
The two Iranians are suspect, but I would DEFINITELY investigate the 2 Ukrainians + 1 Russian on board (3 is a team).. Possibly pro-Putin with a mission to cause a media diversion from the invasion of Crimea.