I always welcome a good conspiracy theory, but this is extremely far-fetched, and (worse) there is evidence to disprove it.
There were some very well know people on the plane (eg. a member of the Dutch parliament, a very well established AIDS scientist), and some from the very town I live in (I know some of their relatives). Incidentally, to keep this discussion vagely relevant to bitcoin, it is the very same sleepy Dutch town in which the recently arrested Silk Road dealer 'Supertrips' and his 3 M$ worth of bitcoin was living (Woerden).
108 of them were going to an AIDS conference.
Most were provably alive shortly before boarding.
So, why would anyone murder these people first only to put them on a plane which is shot out of the sky shortly afterwards? (assuring their death with essentially 100% certainty).
I would imagine though that it isn't unusual for boxes of invalidated passports to be part of the cargo on international flights. Passenger jets carry cargo all the time and in certain instances invalid passports are returned to the issuing government.
The plane departed from the country in which these passports were issued (The Netherlands), so this makes little sense.