The bees are a new addition to the game since I made that post. As you know bees come with Seasons DLC and to calm enraged bees down all you have to do is click on the Bee Box and 'Calm the Bees'. The higher your relationship is with the bees the less likely your sims will be stung. Also bees from the Bee Box are not in the world in general, unlike the FX insects in the base game worlds, the Bee Box needs to be placed by a player.
** edited to add: By keeping a daily routine of bonding with your bees at last twice a day if not more if your sims have time, your bees probably wont reach the point of being enraged. You also have to check that the bees are not needing a mite treatment as this will kill them. Just hover over the bee box with your mouse to check their stats, and click on the bee box to interact with the bees.
