The FI is a way better setup in most cases. High altitude, cold starts and off camber trails to name a few. When Harley Davidson went to the Delphi FI, for me, there was no looking back.
My pickup and Mrs. Lucky's SUV are FI and I wouldn't have it any other way. If there's an issue they go to the mechanic.
I have a carb because it's simple. If something goes wrong, I can fix it. With FI, there's a great learning curve that I'm not prepared to endure. I'm an old retired buzzard and have enough resources that all I need to do is pray, putter and play. If I want to learn something, I'll pick up a guitar.
If you're concerned about the Chicoms popping off a high altitude nuke, look into ferriday cages. Most military vehicles have armor against EMP. Perhaps you can adapt the military technology to civilian use. I doubt that it's any kind of a secret. That might even be an untapped market that preppers would be interested in.
I'm guessing it'd be a lot simpler to create some sort of electronic barrier around whatever components in your Jeep that a EMP would damage, than to retrofit a carb for the extremely remote chance of an EMP.
Cheap and easy is to store your sensitive home electronics in a steel 55 gallon drum that has a removable top.
If there's ever an EMP the local electrical grid would be down and having a running vehicle would be a big advantage, but there's other things that would be more important.
Shelter, water, food, hygiene, security and medicine come to mind. The order of importance depends on the circumstances.
If you research and come up with a way to harden our heaps against an EMP, please post your findings. It would be nice to have a running F-150 in my fleet along side my Jeep.
"EMP Protection" might even be a good sticky in the general discussion forum.
Good Luck, L.M.