I'm not familiar with tornado cash whatsoever, and I'm pretty ignorant about smart contracts too, but I did take a look at the article and I think what needs to happen is for this action to be challenged via the legal system, lest it set a precedent that might put into motion all of those github removals and negative actions against bitcoin that you suggested could happen.
I am not a lawyer myself but haven't we already had such a precedent[1] where the US Government tried to prohibit the distribution of open-source code and where the court ruled out that code is speech and therefore protected by the First Amendment? In this case, the US Government also attempts to censor free speech expressed via computer language, thereby violating the said amendment.
https://www.eff.org/ru/deeplinks/2015/04/remembering-case-established-code-speechBased on the article you cited, the case in question was never appealed, and only cases at the appellate level or higher are actually
case law. However, I do believe that the US Supreme Court would likely agree with the district court ruling.
The problem is that a third party has a long hill to climb if GitHub removes content and is unwilling to fight back. GitHub has its own free speech rights, which would include its right to not publish something. In this case, Tornado Cash developers would likely need to prove that GitHub was acting as an arm of the government when they took down their repo.