The nightkill is exactly the prisoner dilemma for the SK and Mafia. Killing town is considered "cooperating", killing each other is considered "betraying". The only question is how do the players value a draw, compared to a win or a loss.
It is important to note that town loses if there is a lynch, so he is not ever going to vote, unless he values the different losses differently (ex: SK winning instead of Mafia winning, etc.). Which means that the only possible lynch is town. So SK and Mafia can safely choose if they want to cooperate or not during the day, by voting town. If they don't lynch town, they are sending a very clear message that they don't want to cooperate, which means that both will betray during the night, and then town wins.
So the sensible choice is for the SK and the last Mafia to lynch town. However, if a mutual nightkill is ruled as a loss for both factions, then there is no way for anyone to win the stalemate.
This assumes that all players are perfectly rational... which they most often are not. In this situation, I fully expect that considerations about who "deserves to win" will tip the scales one way or another (probably in favour of the SK, since it's usually the hardest role to play).
EDIT: I am assuming that an endgame with only a SK and a Mafia player is considered as a draw for the SK and Mafia, but as a loss for town.
EDIT2: And of course liopoil has already gone over all this quite nicely.