The handling of Barbara Gordon's character (or lack of it?) in The Killing Joke is something that sometimes leads to heated debate.
I think you missed the context of the original debate by comparing to the Wayne parents.
The cover that was used to attract a potential buyer perpetuated the continuing violent misogyny in our society. The lack of sensitivity or empathy towards reducing violence towards women is what's grating, just to make a few measly dollars.
Nowadays, variant covers are a normal part of the sales machinery. Had that cover been offered as a variant rather than as a general sale, there might have been less of an outcry.
As for the story itself - pushing the boundary of 'decency' in making Barbara Gordon a pawn and a degraded victim to affect her loved ones deeply - TV and films rarely go this far. For comic books normally directed at teens, the writers of the book were announcing there are a large swath of adult readers of comic books who want mature themes. In that respect, that proved to be true as the film industry has capitalized with mature themes and comic book heroes.