I always thought Indy and Marion escaping the island was a little dubious, but no more dubious than riding the submarine or pushing over a 30' statue. I just took it with the same grain of salt as Indy surviving a nuke in a fridge.
But, being the geek I am, I've had to reconcile this in my mind at times. Here's my theory: There were still other Nazis at the sub base, but Indy was able to find a radio amongst the equipment in the mountain pass or some similar place and call the British to come pick them up. With their depleted manpower, maybe the Nazis couldn't fight back. Probably some big holes in that theory, like the British being in those waters, but then, the Nazis were in occupied British territory (Cairo) with no fuss . . .
As for the Ark itself, ironically, this is where the movie rings absolutely true: The way of the government and especially the military is not necessarily smart (letting it kill Hitler), but paranoid. They'd do exactly what the movie showed: Lock it up and bury it (along with, as we later learn, the Roswell wreckage).