Oh my gods! Did Ben really kill Penny? I mean, he was at a marina covered in blood and did say to Charles Widmore that he would kill her.
If he did, then Ben really does belong in the son-of-a-bitch category. (And I love Ben!)
I doubt that he killed Desmond, especially after Eloise (the woman at the church, Faraday's mom) said that his part wasn't over. And Ben wouldn't mess with her. Now Desmond will be heading back to the island to kill Ben. (And I do believe that Lost is, in part, a love story between Penny and Desmond.)