I would say either (1) the plague just worked its way through, despite their best efforts, or (2) it was the result of Arthas's conquest of the Scarlet Crusade as seen during the Death Knight starting quests.

Either way, I wish it were explored more. Undead Scarlet Crusaders make for a very interesting contradiction.

They're also undead in (at least parts) of Scarlet Monastery.

I find it perplexing as well... the one group of people able to resist the scourge invasion, staying in stratholme, tyr's hand, and hearthglen while living their crazy cultist lives. Now Arthas is no longer the lich king and they lose that holdout?

Maybe Bolivar actually knows their weakness...

If you were to enter "live side" stratholme, you'd find that Balnazzar had actually resurrected what he could of the Scarlet Crusade, hence why their last remnants are undead in a rather ironic twist.

Also, one of them in EPL says "Undeath is merely a setback!"

I go with the fact that the entirety of the Death Knight starting area is the destruction of the Scarlet Crusade's holdings in EPL, including attacking Tyr's Hand. Combine that with Balnazzar's corruption in Stratholme, and the Scarlets were screwed back in Wrath; I know a lot of RPers who used that storyline, some of them with Scarlet characters.

Like a lot of older Classic plots, though, nothing got updated until Cata, since Tyr's Hand was a quest objective area, and they didn't update the old instances either until 4.0.

There were always some undead in the Monastery; the Graveyard's always been a part of that instance hub, it was just never as popular as the others as there weren't so many quests associated with it before Cata. There was little to no explanation for why the Scarlets had a bunch of ghosts in their own walls, except one, and the details were only given recently with 'The Ashbringer' comic.

Fairbanks likely was infected with the Plague when he lay under a bunch of corpses in Strat to avoid Renault Mograine from killing him while watching the younger man murder his father. Renault had Fairbanks killed when the Inquisitor returned to the monastery to accuse him; Fairbanks' accusations were one of the factors that helped start the Argent Dawn. Poor guy's been locked in that back room in the SM Cathedral since, giving Renault info since he was the elder Mograine's advisor.