Bullets don't harm the nest (atleast fab pistol and rifle) so use a crossbow to break it or send a tamed dimorphodon just whistle attack target at the hive. Ghillie suit makes it so much easier it's almost necessary. I broke the nest no queen, came back later and found one roaming the area. Tried a few times unsuccessfully to feed rare fowers. Use ghillie and bug repellent

and try and come at her at an angle where she's not dead on looking at you and crouch the whole time. Only took 1 flower. If she's angry and the bees attack, back off and try again.