Felt in part that Penny not dying was a bit of a cop out by the writers too scared to do something as dark as that. But when the scene was being handled at this stage I figured Ben mustn't kill her because of the whole judgement thing and that if they were going to go through with killing her it would happen in the season finale.
Probably fitting that she doesn't die because when you think about it, if the Island has a purpose so far much of its purpose leads to people dying. You'd wonder what's worth saving for all that.
Mind, nothing to say he doesn't try again.