Maybe Charley had ALREADY flipped the switch to flood the Looking Glass 1ce before. Maybe since the Others had already failed to stop Charley 1ce that's when Ben went back in time to do it over again and the 2nd time around secretly sent Bonnie and Greta down there to be sure to stop him.

Bonnie and Greta kept asking, "Who are you? Who are you?" to Charley. Could they have been already anticipating his arrival? (Or the arrival of some other Lostie who performed the same function 1ce before??) Perhaps the fact that Bonnie and Greta weren't able to stop Charley is what freaked out Ben so much rather than his just the physically being down there. Maybe the 1st failure to stop Charley was considered a major blunder that had to be kept from most of the Others, so the whole "Bonnie and Greta were sent to do secret work in Canada" excuse was made up to explain their absence when really they were in the Hydra awaiting Charley. Mikhail didn't know they were down there. That tells me that all but the most senior ranking Others didn't know it either.

Furthermore, maybe the 1st time Charley flicked the switch Desmond wasn't with him (because that time he DID give Penny the ring instead of chickening out like Mrs. Hawking advised) and they had the advantage of surprise on their side. Maybe Mrs. Hawking was inserted into Desmond's story the 2nd time around for the same reason that Bonnie and Greta were inserted in Charley's story the 2nd time around??: To make sure all the "right people" get to the island and can't leave it.

Woah! Conspiracies are everywhere! Did you guys hear that Widmore is suspected of being involved in JFK's assasination?