The link contains portions of the script he was working on at the time although to be fair a bit, the script itself is from over a decade ago. He was working on a Batman script during the same time that also got rejected/ignored for Batman Begins instead.
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Originally Posted by Wikipedia
Whedon also pitched a screenplay to adapt Batman for the same company as development started on what would eventually become Batman Begins. It was described as having included a new, "more of a 'Hannibal Lecter' type" villain, and portrayed Bruce Wayne as "a morbid, death-obsessed kid" whose grief was overcome by protecting a girl from being bullied in an alley similar to where his parents were murdered
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Either his vision for comic films changed a lot during the past decade or the script for Batgirl isn't character-destroying terrible which is why Warner Bros is comfortable with it.