Now, maybe you think "breaking in" to a poorly protected network should not be a crime. Maybe you think mass copying of copyrighted materials should not be a crime. But if you take action like Swartz did to protest these laws, you are engaging in an act of civil disobedience and inviting prosecution. And sometimes that's justified, but being prosecuted is part and parcel of civil disobedience.
The rhetoric around this unfortunate incident borders on intellectually dishonest. Our democratically-elected Congress has passed laws, and under those laws breaking into a poorly-protected network isn't any less "hacking" than breaking into a poorly-protected house is trespassing. Those laws also say that scientists own the copyright to their papers, and can license them to distributors, even when their research is paid for with public grant dollars.
The prosecutor in this case pursued her case according to the law. Not some technical "letter of the law" definition of the law, but in response to exactly the kinds of actions the laws were designed to address. Our democratically-elected Congress chose to make those specific things that Swartz did illegal.
That doesn't mean that no one is on the hook. But it's not the relatively simple matter of stopping overzealous prosecution in one agency. The techie community has a far bigger task: convincing elected officials and those that vote for them that there are degrees to "hacking" and that publicly funded research should be freely available. That's the root of the issue here.