I'm generally agree with the posters above. I see the Pathfinder Society as a neutral organization that can (and should) ally itself with whoever it can to advance its own goals. For the sake of balance in the Society, if they ally with good groups, they should definitely make friends with some evil-leaning organizations as well. I would certainly be excited to play a season of PFS that revolved around dealings between the Society and some more nefarious groups in Golarion.
I generally think that the no-evil-characters rule has its place in PFS, in keeping in line some players who would use their character's evil alignment as an excuse to detract from the fun of others. But in the hypothetical situation that either that rule or the evil-leaning factions must go, I'd much rather allow evil characters in than drop those factions from the game.