Look, this show is a social satire, which depicts the "hero" as a complete jerk that doesn't care about anyone, or anything, other than himself. Similarly, it depicts the "villain" to be a good guy who really just wants to make the world a better place, but feels he can't do so without upsetting the "just" class, which is really occupied by cretin "heroes" like Captain Hammer. The letter by Johnny Snow, and Dr. Horrible's response, are not included in the show simply to make a good joke; they are there to show Dr. Horrible's true nature, which is what I have just briefly explained, early in the show without having a narrator openly state it. Hence, he doesn't want to hurt little kids, but he does want to get into the Evil League of Evil.
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