Nope, you have the right idea - somehow this turned into "are they going to kill Indy" rather than my intention of discussing how people here would like to see his end handled.
I'd forgot about them pulling the scenes from the DVD's - interesting, but I still don't think personally that they'd kill him. Lucas is certainly not a capable enough anything (producer/director/writer etc.) to pull of something like that, even with Speilberg's help. I still contend though that done right, it could be a moment that would live in cinema history much longer than KOTCS is likely to last.
As to why you'd kill him off? Other than the obvious psychological closure, and the truly heroic nature (I prefer my heroes dying the way they live, rather than tottering around forgetting their own name and crapping in a diaper), there could be a financial reason. Clearly, they want to make the transition from Indy to Mutt. Their wouldn't be a Mutt in this film if that wasn't the plan. Having Indy live might be the nail in the coffin of those plans however. As long as he does, fans will be less willing to accept a replacement. In fact, I think they'd be more willing to accept another actor in the role (ala James Bond) than accepting a new character like Mutt. However, kill him off (and do it the right way), and people might be more accepting of Mutt in future films. Just food for thought.