That flight was during a period when the Soviet's were terrified of a US first strike.

Not long after this flight was the Able Archer 83 exercise, which is probably the only time since the Cuban Missile crisis that we got close to an actual nuclear war.

http://en.wikipedia.org/wiki/Able_Archer_83

Of course, no excuse for shooting down an innocent airliner, but it's often overlooked just how scared the Soviet leaders were at this time.

Again, not space program and reasonable suspicion of spying.