They're not actual achievements - I believe this is to do with the Apiarists Databank and the number of species you've discovered.
It's weird that that was the first time I saw that kind of achievement because I started breeding bees a while ago.
Oh god... I don't even... What have I done?!? I put three of them in there for safe keeping and now I don't even know how to deal with this.
Are you using an auto spawner? If so, turn it off (redstone signal or just don't give it anymore power) and then use:
Lava, water (cover the room, so they'll drown), splash potion of harming or dig out a hole under them and make them fall. If you want to be a little bit more creative: MFFS (force field) with a Projector Upgrade (Defense Station), dig out a hole and use a Conveyor belt to transport them to spikes, use a portal gun, shoot it at their feet and transport them somewhere else,... You could also try holy granades, they don't destroy blocks and do a good amount of damage but I'm not sure if they'll hurt villagers.
But be aware, it'll most likely cause lag if you kill many of them at once.
You could also use it to your advantage first by making a trading posts to get lots of emeralds.