It was not a real option. He had run out of money for an expensive, complex case. He was sure to lose.
For someone of Aaron's talent and reputation there is no reason that he could not have gotten past a felony conviction and lived a successful life.
I can only interpret Lessig's post:
"...the question this government needs to answer is why it was so necessary that Aaron Swartz be labeled a “felon.” For in the 18 months of negotiations, that was what he was not willing to accept..."
I don't know what the government actually offered, but it doesn't seem unreasonable that Aaron would have been able to get a deal with a relatively light sentence, maybe just probation. It sounds from Lessig's post like his hangup was that he wasn't willing to accept a felony conviction. I hope that's not the case because even with a felony record he most likely would have lived a long and successful life.
Being sentenced and getting a record for doing something you feel is right is not something everybody takes equally lightly. Personally I couldn't care less but I can see how someone with stronger principles would react much stronger to this.