The "world-building" explanation is all well and good, but I'm sure Reeves is smart enough to understand the implications that come with letting the Joker genie out of the bottle. You don't go out of your way to hype up a deleted scene with that character, then proceed to release that scene online after a weekslong viral campaign, unless you are planning something to come. And I doubt Reeves put all of his eggs in the Arkham series basket. Not with a character this significant to the mythos.
My gut? We're getting The Joker as a main antagonist in one of these films. Whether as a solo villain, or one of several villains. Either way, he's coming. The release of the deleted scene (and all the fanfare that went into it) removed all doubt in my mind.