If Nanaya's above you and you're on ground and he has thrown out a jc, then block it. It's not the only choice, but far far better than any others. Blocking is very practical since, as you have stated, Nanaya's jc even stuffs shoryus.
Nanaya's jc has massive priority, but it has a distinct contact point of below him. That hitspot is smaller than you think, and the move comes out relatively slow, also. You can avoid having hard time with it by maneuvering your character so that such situations don't occur. In fact, try playing Nanaya against a computer and try to land jcs. You'll be able to find the many weakness of the move through that.