I can totally understand the government not trusting the people to deal with it well, if indeed they did shoot down flight 93. But I think that in general people would have understood, or could have been made to understand, the terrible calculus of war. Deciding that these hundred people must die so that these other thousand people might live is terrible, but generally people will forgive leaders for doing it (cf., nobody calls Churchill 'the Butcher of Coventry')
Most heart-wrenching is the idea of the passengers successfully overthrowing the hijackers and *then* getting shot down *anyhow*, due to not being able to successfully communicate that they were in command of the plane.
*That* is a story I think the government would cover up, even though in practice it is no different than the case where the passengers are all killed or subdued and the plane/weapon is still on its mission.
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