Note: "pygmy" is often used as a pejorative but there isn't a good catch-all term that covers all of the Mbenga/Mbuti/Twa/etc. peoples so I'll stick to using it.
Here's my shot. While there are a lot of challenges for this wank the extent to which the pygmies have been screwed IOTL makes even a pretty marginal result a relative wank.
Let's start off with bees. IIRC a lot of the non-Bantu words in one of the Mbuti languages related to bee-keeping. For the POD someone figures out how to make a rudimentary bee gum by hacking hollows in trees for bees and then covering them with leaves to keep the rain out.
Even really basic beekeeping provides a few more calories and people figure out that maybe hacking hollows into trees that produce fruit isn't the best idea for from there you get people targeting non-fruit bearing trees for use as hives leading to more organized culling of trees that don't produce anything tasty.
This isn't agriculture, but it could get you to a fruit-based horticultural system in which fruit (or nut) trees are allowed to grow and other trees are removed bit by bit, which seemed to have happened in the pre-Columbian amazon. Having more fruit trees also means more bees and that'd give people an incentive to burn more wood to control the bees. That could eventually set the stage for Congolese terra preta (artificial Amazonian black earth that was made out of pottery shards and charcoal IIRC) at a later stage.
More fruit trees means higher populations and larger and more permanent settlements which'll bring rats. Rats are a good ATL target for domestication, filling the rabbit/chicken niche and providing some protein (for a gimmie I'd probably go with tamed but not really domesticated grey parrots). Add to that some basic aquaculture (weirs etc.) to get fish and you could get substantially higher populations once the Bantu or their equivalent hit.
Hunter-gatherers don't tend to do very well in the face of agricultural expansion so the Bantu will hit the pygmies like a ton of bricks, as IOTL. With larger populations the wanked pygmies would be in a better position and with more fruit and honey they'd be in a better position to offer tribute in the form of fruit wine and mead (everyone loves booze).
Any other ideas? Would love to expand this into a full Lands of Red and Gold style TL (Lands of Trees and Bees?) but personal life really isn't going to allow that so spitballing is as far as I'm going to go.