OH JOSS WHEDON NO
I loved Dr. Horrible. Adored it. Squeed like mad. Which is why I am right now so angry I want to punch Joss right in the mouth. I stupidly thought Joss wouldn't go there (again). And if he was trying to make a commentary on that issue, I think he massively failed.
My problem with the fact and way Penny died is that Joss pulled a classic "women in refrigerators" move with her, which I find inexcusable since Joss presents himself a feminist ally and he's versed in superhero comics.
He should damn well have known better, known that he was using a comic trope that is all about writing women out of the story, about valuing women only for their use in motivating the hero and is one of the biggest issues feminist comic fans have with the genre. And I think I'm as pissed at myself as I am at Joss for stupidly assuming he wouldn't go there with this, that he'd understand the context of killing Penny the way he did in a superhero comic would make him look like just every other sexist comic writer who disposes of women for no good reason.
The only thing he did different with the trope was that the hero and the villain were the same person.