When this was first reported right after 9/11, I don't remember there being anything said about someone having been shot. It just said that the passenger was killed by one of the hijackers, presumably with the box-cutter used on the others. Maybe the Al Queda guy found out that Lewin was Jewish and decided to kill him first presuming that Lewin would have had military training thus would be a threat to the hijackers.
But if the story had mentioned a gun, I probably would have remembered it, also wondering how they'd gotten one on board.
Well, they just arrested 20 folks at Boston's Logan Airport (where this flight originated) with forged identities that had " access to all areas of the airport, including terminals, baggage areas, screened passenger checkpoints and runways."
I'd say that with the "secure" folks being that badly screened (if at all) it might not be too hard to have the cleaning/food services guy put a gun or bomb in the seat cushion/toilet/magazine rack/whatever.
Or maybe a gun was planted in the terrorist's bag far away from the plane by a mere baggage handler or a team of security screener(s) inside the airport!!!