Well, you can't assume that everyone in the Alliance has the same knowledge about the Scarlet Crusade as the player. The Church NPCs in the Cathedral of Stormwind still deny that Benedictus was the Twilight Father if you speak to them. Back in Classic you also quested for a Scarlet Emissary in Desolace who seemed to know very little about the corruption that had taken hold of the organisation. The "wiped out" thing is also hardly a defeater for the Scarlet Crusade since they've been "wiped out" in Classic, WotLK, Cata and MoP and still somehow manage to return every single time (not saying that this is necessarily good but there's definitely precedent for them rising from the ashes).
I think they're aesthetically distinct and would provide some interesting friction to human society while functioning as an outlet for all the Alliance players who don't want to "cozy up" to the Horde.