Its been revealed that, amongst a long list of other changes to go from an "M" rating to the much easier to market and sell "T" rating, the Joker's fatality in MK vs DC has been changed and now the actually shooting occurs off screen. He still pulls out his gun and has the "BANG" sign come out, but there will be an abrupt camera jerk to take the action off screen and have the Joker do the deed to the poor sap away from our innocent eyes.
Apparently this is one part DC wanting to not "tarnish" their characters too much in this version, as well as Midway wanting to actually sell some copies, as the series has become rather disappointing in terms of sales in recent years and this is basically boiling down to a publicity stunt to move as many games as possible.