A lot of good jokes in this one!
I'm telling y'all, though, Indy was not still wanted for murder by the end of the film. That all got resolved with the American military extraction of Voller, Klaber, and Hauke from Morocco. Mason witnessed the murders first hand, and she likely helped orchestrate the extraction. She chewed them all out on the helicopter, and the dialogue in that scene made it quite clear that the three of them were in major trouble with the US government.
If that wasn't enough, Indy needed the dial, and Helena, in order to prove his innocence on his own. Helena easily could have gone to the police while he was knocked out at the end of the film to clear his name.
But it's the first one. Really it's the first one. It's just too obvious for me.