In SC3 you could interrupt the 2 hits with a really fast move (there was a double hit at about i13 or even less) and TJ over the 2nd hit. To make it short: you punish it a little but are sure of it or try to punish it for more dmg (maybe you can do 8B+K~DGF B with Yoshi). 236A alone is quite punishable, of course, but you won't be able to punish it with 9K or 8B+K~DGF B AFAIK.
I've seen some people posting that you can react to whether your opponent does 236A or 236A,A (the difference in the animation of Sophie when she's in air) but I haven't seen somebody who can do it.
With Yoshi you probably have good options against it (I think that delayed iMCF is the best here - NH punishment or CH comb) but I yet haven't looked into this character this much to be sure how to play against Sophie's 236A,A.