Bees seem to be pretty rare when you first start the game. In my latest game I only had 2 hives in the whole world. I hadn't run across the killer bees yet, so not knowing they were different than the regular bees (even though they were red) i collected 4 of them and then broke the hive. Upon realizing that i couldn't use the 4 bees I collected to craft a hive i went exploring with for another hive. When I found another hive (i had picked up some pig bros) no bees were flying around so i ran up and punched the hive. About 8 killer bees and then 1 yellow bee came out and while I was running around dealing with the bees the pigs killed the hive. That was unfortunately the last hive in my world. So now I am at day 36 and have no hives and only one yellow bee. So here's my suggestion...
-Suggestion 1 -You should either be able to tame killer bees (maybe with a special hive that doesn't require bees to craft) or just be able to craft a killer bee hive. I think the killer bee hive would work the best, even though it will be a little tougher to get the honey since the killer bees do extra damage.
-Suggestion 2 -Another option would be to have bees very rarely spawn from flowers.
-Suggestion 3- One more possibility would be if you collect and planted enough flowers in an area then a bee hive would eventually spawn if no other were on the map.
The main reason for the suggestion is now i feel i have to start my world over since i wont have access to honey, all the foods you can craft from honey and sleeping darts. But if either of the suggestions above were implemented it would not be a world killer if you mess up your bees in the early game.