I'm not sure if this is intended due to turbulence in BH&H II thanks to how light most of the aircraft are, but every now and then, my plane will get very violently tossed around. This almost always manifests as a very hard pitch up that not even full down elevators can counter, lasting until I lose all momentum and stall, and often happens multiple times in quick succession. The odd thing is that it occurs even if I disable wind effects for player aircraft. Does anyone else notice this happening, and is it intended behavior? It makes flying long missions quite difficult.

There is turbulence as you fly, but usually wouldn't be that bad. I haven't seen that so bad.
Try staying clear of flying through the larger clouds as inside a cloud be can be dangerous - also so in real life in a small aircraft avoid bad weather. Recon Wars patch would normally stop you flying in bad weather unless you override it.

Maybe also check your the controller - if you run WOFFkeys tool in woff\toolbox you can see if axis are active when they shouldn't be for example.

I feel very silly now, it was the controller settings! Apparently pitch was bound to a few more axes than I was expecting, so I've cleaned that up now. Thanks for the help, it's great that you guys are so responsive!

Excellent glad you found it.