In libertopia... Aaron would only face life in prison if he entered into a contract with MIT agreeing to life in prison for accessing the systems in the way he did.
In libertopia... you cannot consent to terms you cannot negotiate (IE accessing a website does not magically enter you into some agreement).
Second, the root of the CFAA charge wasn't intellectual property, but physical property: MIT's network. Libertarians certainly do recognize non-contractual violations of property rights, i.e. various incarnations of trespass.
Arguing that violation of property rights is justified by some greater social purpose is distinctly unlibertarian.
As for "abuse" of the process, that's orthogonal to libertarianism. Classic libertarians believe in limited government, but once the legitimate object of government is implicated, in this case protecting property rights, they do not have any tendency towards favoring more forgiving or lenient prosecution.
Under a Libertarian regime, the whole thing would've been simpler, as no theory of justice or societal good would've been involved. It would've simply been JSTOR and MIT extracting whatever revenge they'd considered.
Let me illustrate. Say you belong to a private club. The contract of membership allows you to use the clubhouse, as long as you don't bring any Hindu guests. Say one day you do. That's a breach of contract. Say you come back the next day. Since you've breached the contract, your license to use the house is revoked, and now its an infringement of property: trespass. Finally, lets say you punch the owner for being racist. Any classic libertarian will support prosecuting you under three legal theories: breach of contract, trespass, and battery (a tort). Classic libertarians don't reject any of these.