If I was enroute I'd start planning on diverting or turning back depending on location. I'd also throw up our window shades and advise the cabin to lower theirs.
The thought of getting on the ground ASAP or far enough way would also be of thought as our aircraft are not hardened. Hell if it was real I wouldn't discount flying on the eastern backsides of the islands. EMP is mostly LOS.
Your basically choosing to either climb and run or descend and hide in my view. That would be a tough call and it would depend on time since launch, location and numerous other holy **** factors! Our military guys would have better answers.
One thing is for sure! I'd have my sunglasses on!
Hopefully we' only be dealing with one crazy a$$ MF launching one missile. If China or Russia joined in or Trump got trigger happy well everything above is null anyway!