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Supposedly in regarding the Killing Joke, Alan Moore himself actually expressed regret working on that one, in particular for what it did to Barbara. Thoughts on this?
I agree that everyone should be uncomfortable with how Barbara Gordon was used. She was objectified, pure and simple. After being Batgirl for a lot of years, she was stripped of any sense of strength and used solely as a victim.

There was almost nothing of Barbara Gordon here, just a female body being used as a tool.
It gets worse from there as Barbara is posed nude. Why? Because Jim Gordon needed to further traumatized? No, not really. Showing pictures of a bleeding, shot but clothed Barbara would have worked just as well.

Part of it was the time period in which the book was done (1988). This kind of semi-erotic pandering was still considered more or less acceptable then, particularly in an age when DC was trying to establish itself in the adult (as in grown ups with money to spend in their hobby) graphic novel market. That said, the sexual subtext was completely unnecessary to the storyline then and the passage of time has made it more inappropriate when looked at today.
It's ironic that this twisted rape fantasy gave rise to one of DC's strongest female characters - Oracle.

To be honest, I will always prefer Oracle to Batgirl but that doesn't make what happened right.
So yes, Alan Moore should feel bad about what he did to Barbara Gordon in The Killing Joke. DC took a capable female superhero and objectified her. It was wrong then and it's still wrong now.