Well yeah, Nubia is always going to be at risk of an instagib as it's in the de jure lands of egypt. The rest of ethiopia isn't though. To hold nubia for any length of time you'll need to severely weaken the caliph of egypt.
Being part of de jure Egypt is seriously hurting Nubia and I'm also one of those who think that it doesn't make sense. It did make sense when all other small kingdoms were titular, but now there's even small fantasy kingdoms. I think Paradox should make Nubia de jure kingdom and it would help a lot. I haven't tried them in 1.08, but in 1.07 I got annoyed when in 5 games in a row Egyptians attacked against me in 1066 and Axum finished the job.