Maybe it's my one tracked mind, but there was one scene that definitely seemed like a reference to the SBVT attacks in '04. The film takes place during the fifties and the McCarthy era. Indy gets captured by the feds after being detained by the Soviets; some of the feds are basically McCarthy right wing goons, and question whether he is a Soviet spy. An Army guy walks in, and vouches for Indiana Jones, who had served in the OSS in WWII. The goons keep still questioning his patriotism, and the Army guy, outraged, says "Have you any idea how many medals this man earned in the war?!?". The goons replied, "That's IF he deserved them". For which Indy gives them a major look of death.
I checked the history of McCarthy and the Army hearings:
http://en.wikipedia.org/wiki/Army-McCarthy_hearingsI didn't see anything to indicate that it was common for him to question if they deserved getting medals; just if they were a communist. That is why I think my gut instinct is correct -- that George Lucas put that in the film to refer to more recent times. Remember he did that in the last Star Wars film he did, too.