I don't think you see the difference, Aaron was downloading the data off of MIT servers himself, he was not facing charges for writing the scripts.

From your link:

The Justice Department's press release announcing Aaron's indictment suggests the true motivation for pursuing the case was that Aaron downloaded academic literature from JSTOR and planned to make it available to the public for free as a political statement about access to knowledge.

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Tools that can be used maliciously are generally allowed because they have legitimate uses, using them to gain access or otherwise harm a computer system or network without authorization is criminal.

As I said before, Beeper users are gaining unauthorized access, not Beeper. It is E2EE, they're not the middleman.