I can't find all of the facts yet, but it appears that the hometown Dodgers have handled a swarm in the stands with far more humanity than the Padres did. The team simply cleared people out the swarmed section of stands and left the bees alone.
The rationale for this may have been based on a goat-removal curse that vexed the Cubs for years, or maybe they learned something from their rivals to the south.
What they did with the bees after that I do not know. Will do my best to get in touch with the team and find out.
Here's a link to the story from LA Times