Passengers were in danger in a same way passengers are in danger over New York if pilot refuses ATC directions.
Yeah, Morales's pilot could choose a different path provided there's air refueling available. Otherwise it had to land somewhere, and then airplane was searched. I'm pretty sure there are conventions that forbid that kind behavior against diplomatic personal.
So, in the end, we are again at the same place - when we ignore conventions that's perfectly fine, and when they do the same it's a completely different.
btw read first article of Chicago convention, then check what sovereignty means.