The video looks like pretty normal basenji stuff. She was better when you weren't right there petting her. The more you say 'oh, pretty girl' etc, while she is growling, you are reinforcing that behavior….she thinks 'oh, he must think I am doing the right thing, because he is saying nice things to me'. The most I will say to the growling dog in this situation is 'oh, you are okay, give it a rest'...but not in a praising voice...just quiet recognition of their torture
She wants him to get off of her, and he isn't getting the message. Eventually, he will. She is giving him a TON of warning before she snaps, and that is ideal.
For the most part I would just stay out of it. If you feel like you must intervene (and I can understand that), I would just walk over and pick up the puppy, carry him somewhere elseand redirect his attention (play a game with him, or give him something to do). That way you are telling him 'when she makes this noise, it means leave her alone'
They are both behaving appropriately for their age in this video, IMO.