One of the hottest topics over the last few days has been the thought that Batman: The Killing Joke was supposed to be comics canon, or should not have been canon. My thought? Comics canon is only what readers consider to be comics canon.
Who Makes Comics Canon?
Comic book creators do not create canon. Comic book publishers do not create canon. The only ones who do are the readers collectively. There have been many times in which comic book companies have attempted to backtrack on certain aspects of created canon, but it has not worked. You, and I create canon in comics and nobody can take that away from us.
Your Opinion
If you believe Batman actually killed Joker in the final pages of the graphic novel, good for you. I am not going to say that you are wrong because it is what you believe to be true. I might wonder how you accept that Joker continued on in the comics afterwords, but why argue? It is canon for you.