Github can't reasonably he considered one of the parties in this scenario, the owners of the circumvention technology would be.
It's not that users are irrationally responding to DMCA requests when they don't need to, its that as a service provider, GitHub defaults to a stance where a claimant's DMCA is automatically processed if a repo author doesn't reply within 1 working day. This effectively means that for DMCA requests of all types on GitHub, "no response" is synonymous with "I'm guilty of infringement, plaese take down the content".
A DMCA claim response in GitHub is admissible as testimony should the case ever make it to court, and therefore carries the penalty of perjury (both parties are informed of this before opening/responding to the claim in the GitHub UI). So unless the repo author is absolutely certain that they're not hosting DRM circumvention software, they have little-to-no recourse but to allow the takedown request to go ahead.
All of the safe harbor provisions and takedown measures have to do with hosting copyright infringing material. They make no mention of needing to do anything if you're hosting DRM circumvention technology.
By your logic, I could submit DMCA takedowns over libel and the service provider would have to take it down despite it being obvious that libel is not part of the safe harbor provisions.