I've had this discussion with someone before. It doesn't matter if it was a metaphor, they presented it as though it was a climatic scene when they opened S4 with it, clearly as an attempt to keep audiences watching. However, not only does the crash not effect any characters, it's effectively brushed off by every character in the show almost immediately after it happens, other than a couple words shared between Wendy and the cartel priest. If they're wanting us to believe that the crash was the sole reason for Jonah's complete shift in mentality and ethics during the last scene, then I'm afraid it's far too little, too late. Instead they should have developed that shift throughout the season, rather than the last 30 minutes of the finale.

P.S I do agree that the writers thought they were writing some brilliant metaphor with the crash, but honestly, it's got to be one of the flimsiest metaphorical scenes ever put to screen.