I think this is being handled the right way now by the Internet Archive. Sort of like a library that keeps old copies of newspapers around on microfiche, or a museum that has samples of bugs in Indonesia 100 years ago. They have a dedicated mission to preserve, around which supportive people can organize effort and money.
I don’t think this can be solved by decentralized protocols. A lot of folks just won’t put in the effort. Quite a few companies already actively delete old content; there’s no way they are going to opt into web server software that prevents that.
Expectations are set, not interrogated. Let me give you an example
Companies and organizations with domains are expected to also be running mail on that domain.
Why? I can sit around and make up a bunch of reasons but none of them are given when that mail service is being set up, it's done out of expectation, just like how someone might pay $295,000.00 for the .com they want and wouldn't even pay $2.95 for the .me or .us
Are the .com keys closer together? Easier to type? Supported by more browsers? No.
There's mostly arbitrary social norms that get institutionalized.
They can go away. Having ftp service or a fax line, for instance, used to be one of them. Those weren't thrown into the trash for cost cutting reasons, the norms changed.
The question is where do we want these norms to go and what are we doing to encourage it?
This is how this could materialize - say there's an optional archival fee when registering a domain. Next search engines could prioritize domains that pay this fee under the logic that by doing it, the website owners are standing behind what they publish.
These types of schemes are pretty easy to fabricate - the point is the solutions are plentiful, it's all a matter of focus, effort and intentions.
I don’t think this can be solved by decentralized protocols. A lot of folks just won’t put in the effort. Quite a few companies already actively delete old content; there’s no way they are going to opt into web server software that prevents that.