If Jacob is the good (light) side and the mysterious stranger tonight is the bad (dark) side... then does Locke's proclamation that he's going to kill Jacob mean that he is really an agent of the Dark Side???

Or is Locke merely playing Ben/Richard so he can free Jacob from his Prison (The Cabin)???

Killing Jacob might be the way to free Jacob..

That's not Locke leading the Others and killing Jacob. It's something else. Locke is dead.
The appartion, body, whatever, that looks like Locke apparently contains the essence of the man who was in the opening scene that wanted to kill Jacob. Whether he's good or bad probably depends upon perspective and might change in S6, but right now I'm pulling for Jacob and his team, which probably includes the Losties, to whom he was referring when he said "they're coming".

Well, Locke can't be an agent of evil since Locke's dead. That's Jacob's opposite from the opening. That's why they show us Locke's corpse on the beach.