Now at first I thought Ben left the church and then went and killed Penny, thus Desmond beat the hell out of him. But when you think about it that way... that's just plain silly, Des would not hesitate to kill Ben for a second if he had killed Penny. So then I thought that perhaps he only hurt Penny and Desmond got to Ben before he killed her. However the more and more I think about it, I think that Ben did indeed kill Penny. Desmond did "kill" Ben, or so he thought. However we've seen the Island choose to heal Ben since then, so clearly it is not done with him yet. The island did not allow Ben to die. My guess is that now Desmond has turned to Widmore... the only man he knows can help him return to the Island. Desmond now knows the "rules" don't apply to him, this knowledge mixed with the bit he got while listening to Eloise Hawking will lead him to the conclusion that he can change what happened. He MUST return to the island if he ever wants a chance of seeing Penny again.
Just some thoughts... what do you guys think?
p.s. If this is true at all... then the writer's will certainly have some fun stories to work with for season 6. Ji Yeon, Aaron, Charlie, Clementine... there's gonna be a lot of kids looking for Mommy and Daddy in the not too distant future.