Yeah, I mean, there's basically three options for four-player: 3v1 with a handicap, 2v2 with a handicap, and 2.5v1.5. 3v1 seems kinda boring, and 2v2 would be really difficult to balance (though if anyone does try 2v2 with an altered jump track, I'd be interested in hearing what happens). So the question is how to specify half a cylon. The problems with the sympathizer, as I see it, are twofold: 1) metagaming and 2) it's less fun to play a hobbled member of your team. (Personally I'm more annoyed by the second of those, but YMMV.)
The agendas from Pegasus do a pretty good job of fixing both problems, by giving the player a goal that partly helps the humans and partly helps the cylons, and replaces the intrigue of "which team are you on" with that of "which goal do you have." The main complaints about it have to do with the details of these agendas; namely that some are far more pro-human or -cylon than others, the range of agendas creates less intrigue than there could be, and the other players don't have much reason to interact with you. The good news there is that you can't heave a brick on the BGG forums without hitting about a dozen fan-made variants, some of which are pretty good. So it wouldn't be difficult to implement one of those (or create your own) without owning Pegasus, just treat the sympathizer as a Cylon with a randomly determined agenda.
I know people have also experimented with having an unpredictable sleeper agent phase; I don't remember how, exactly, maybe after each unit of distance you roll a die, or maybe it's secretly determined at the start of the game, but that prevents people from gaming both the dials and the sleeper distance itself. Of course, there's no telling what kind of balance issues this would introduce.
I'm just thinking out loud here.