Has a scheduled passenger flight ever stalled because of shifting cargo?
Yes, a LET-410 crashed in the DR Congo, apparently because a crocodile escaped. Passengers trying to escape the animal apparently caused enough of a load shift to result in a crash.

Not a shift, but Air Midwest Flight 5481 crashed due to a combination of a  weight and balance error coupled with a misrigged elevator.

In general, it's harder to have a significant load shift on a passenger aircraft since it's easy to check the distribution of passenger loads, people are well restrained by seat backs, and unless something else is catastrophically wrong (fire), passengers don't all get up and move to one side of the aircraft.