Alex Stamos doesn't even really try to refute that. Instead he provides context that suggests that it was an injustice to apply those laws to Aaron Swartz. That's a separate question, and one that Kerr apparently intends to address in a follow up post.
Which is its own problem. But the problem with what prosecutors did is that prosecutors are allowed not to bring the charges and did anyway, notwithstanding the epic disproportionality of the charged penalties to the acts.
In other words, the problem is that the law is defective, and prosecutors could have had a conscience and not abused that fact to break this kid, but they failed at being human, and for that they are culpable. Morally and ethically if not legally.
While we wait though, I wonder Aaron's lawyers ever explained to him that thirty five years was an all but impossible outcome of this case, that seven years was a longshot and some type of non-incarceration a distinct possibility. If his lawyers for some reason didn't make that clear they did him no favors.
Now whether pervasive overcharging to extract pleas is itself ethical is another question ...
Now admittedly I'm not an expert at internet law (though I do have a JD), but Professor Kerr is. Unless your contention is that he doesn't understand the technical details well enough to render an opinion, I don't see how you or the linked article refute his opinion given that you neither of you address it head on (i.e. using the case law).