Sean Burns would be a good choice, and he's rarely a main character in fics. You'd have to ignore his canonical death, though. Was he in any episodes before the one in which he died? I don't recall.

Or maybe they take Methos. Because, you're right, Duncan doesn't exactly have a good track record of getting along with headhunters, but Methos actually does. He was part of the Horsemen for a thousand years without killing any of them, he goes out of his way to avoid challenges now, and he helped Duncan recover from the Dark Quickening. He also knew both Darius and Sean but with no details in canon, a fic could come up with all sorts of backstory.

Of course, Methos would probably be even less pleased than Duncan by being kidnapped by aliens and left with a bunch of headhunter aliens in stasis pods. Heh.