Note: Short attention spans, please move to the next post.
The DC Universe is written in a recognizable way to us, in that the overall structure of reality is intact, the physical world maintains the same look and feel, and people are people (more or less). We can assume that there is gravity and physical substance and hunger. The things we take for granted in the real world are present, but not typically as a centerpiece in comics.
Also present are fantasy elements to make the stories appealing to readers. We read because amazing things happen in comics, not because the content matches real life so well. Even characters like Batman who aren't superhuman are fascinating because they still achieve "amazement" levels through their intellect, determination and resourcefulness.
The reality and fantasy in comics are meshed by writers who don't necessarily have a complete and thorough understanding of their topics in the real world, and therefore have to contrive justification for what happens via the fantasy elements. Additionally, they write within the framework of comics being a business. They have a job. Stories must be written, but deadlines must be met so that comic books can be sold. Neither a consistent and accurate characterization nor maintenance of continuity are entirely possible. We talk about CIS and PIS to cover these very things.
So a discussion about how Batman should handle the Joker must be done within the context of it being a comic book story written by people in the real world who want to continue to have jobs. Is Batman's logic about killing going to be absolutely sound?
It's easy enough to look at one element of a character and make a decision about what "ought to be done", and even if that decision is justifiable on its own, the impact to the rest of the comic book world in which that character lives has to be taken into account. The writers are effectively the (albeit, imperfect) gods of their comic book universes, which you might look at as a struggling pantheon, since they each have control only over certain characters and themes. But they have to consider the butterfly effect of those characters' actions, and the more major the action, the worse the effects would be.
I mean, holy crap. Trying to juggle what's exciting, cool, intriguing, reasonable, in-character and consistent ain't easy. Of course they screw it up sometimes, but such a major move like Batman (or anyone) killing the Joker takes some serious consideration.