Batman killed people in the Burton films, and that still never bothered me cause its a movie.
Same as it never bothered me that Punisher was set in Miami, or Doom was on the rocketship with the FF.

Only times I hate stuff is when it adds nothing to the film itself, like introducing Gwen Stacey in Spidey 3, when it added nothing to the plot (they could have made up a character for the role she played).