The FAA standards are generally much looser, but when it comes to incapacating conditions they are right up there with the military: DQ

With that said, you have more control over how you present your case to the FAA...one approach might be to go find a civilian specialist who will support your idea about the cause of the seizure, vigorously and in writing. Keep looking until you find one, then go to the FAA with all the supporting docs.

Also off the top of my head, high fevers and infections may also cause seizures...might be avenues to explore.

There are several companies which offer fee consulting for FAA medical issue, they are staffed by ex-FAA AME's (no longer obligated to report everything they hear to OKC). Virtual Flight Surgeons is one, they are used by ALPA.

My guess with the airlines is that if the FAA agrees that it was a transient condition caused by meds or illness, they won't care about it.

BTW if you want an airline job you will need a First Class Medical. That also applies for most of the best non-airline jobs too. A second class basically just allows a pilot who used to have a a first class to keep his job after he develops some condition.