Other than air-gapping, does anyone know enough about rule 41 to provide advice and guidance on how to protect a linux system from this type of remote hacking? I've read that perhaps linux + disk encryption + firejail with Tor could possibly be a good defense. I've also read that booting and running from a liveCD would be the only way to prevent such access to your system.
This answer covers only the recent changes to Rule 41, which I assume from your links is what you are asking about. It also assumes you and/or your equipment is in the US; if you're a non-citizen and you and your equipment are outside the US, the 4th Amendment rights that are clarified by Rule 41 wouldn't apply to you anyway
The changes primarily affect the (geographic) scope of what law enforcement is legally allowed to search with a warrant. So it's worth pointing out that you're asking for information on how to prevent agents of the government from legally obtaining information from your system that they have been explicitly (via a warrant) been given permission to have.
From a technical perspective, there's no difference between
- a) what law enforcement from within your jurisdiction is allowed to do (and has been allowed to do) regardless of Rule 41 changes,
- b) what law enforcement from a different jurisdiction is now allowed to do under Rule 41, and
- c) what criminals can do outside the law to hack your computer.
So from a technical perspective, this question is just, "how do I secure my computer from access by people who were not personally authorized by me to access it," and the Rule 41 part of your question is irrelevant.
Finally, it's probably worth noting that the changes to Rule 41 include allowing a judge from outside your jurisdiction to issue a warrant if "the district where the media or information is located has been concealed through technological means," so using Tor would actually bring you into the scope of the Rule 41 changes; if you don't hack (damage) someone else's computer and don't try to hide your location then you are not affected by the changes to Rule 41.