Not to sound like too much of a cynic...does anybody really think, from a business standpoint, WB would really cut a scene as polarizing and controversial as Ledger's Joker in a body bag? To clarify, I'm not saying that WB is a bunch of emotionless drones, but it's something to think about.
To cut this would upset a good deal of the fans they've specifically targeted with their viral marketing and would isolate a lot of people who have invested a lot of time in the hype leading up to this movie. If this rumored scene is in fact at risk of hitting the chopping block, I'm sure the studio would run it by Ledger's family first - and they've unequivocally said they want this body of work to stand by itself in its current form.
They have too much to lose if they cut it and any bad press that Nolan, WB, or the rest of those involved in the movie's release would receive will be far outweighed by what they have to gain by keeping it in.