Did you start right off fighting the bees, or talking to them? To get the pure honey, you need to talk to them and refuse to take their eggs until you get the option to explain why you won't take the eggs. Choose duty, and you'll never have an eggs encounter again, just pure honey. Also, if you've talked instead of fought every now and then (before the why no eggs choice) the bee girl will have no eggs but will offer pure honey if you get her off.
If you fought her instead, then you'll need to gain access to the Bazaar in the plains (33+ corruption required for initial entry, no corruption requirement for reentry) and keep an eye on Benoit's shop each day. Pure honey is one of the things you can find there iirc.