Earlier quoted context omitted.
Should you always plead guilty to crimes the Government accuses you of?
No, but if there's prima facie evidence of criminal activity (such as the surveillance video, being caught red-handed with the laptop), then maybe you should consider it. Effectively the government was asking him to face up to the fact that whatever his views about the ethics of JSTOR were, the way he acted upon them (breaking into a wiring closet etc.) was illegal. It's not like anybody contests the facts of what he…
For instance, the trespassing charges, supported by the surveillance video of him opening an unlocked closet used by the homeless to store their personal effects, were dropped. [1]
[1] http://boingboing.net/2013/01/13/expert-witness-describes-aa...