As far as Let’s Encrypt goes, the easy way to solve that is self-signed SSL certificates and Tofu. Just make it stupid obvious if an SSL certificate changes on a site that you go to. Like, turn your browser into a giant red screen that says that the security of the website has changed and may be broken obvious. Maybe you could have search engines also index SSL certificates so you could see if Google and Bing and DuckDuckGo and whoever else all say that this website has the same SSL certificate that it has had for X amount of time and if the search engines start showing different results you get suspicious.

Edit: Using self-signed certificates and tofu fits better with the decentralized ethos of the original web anyway since you’re not relying on some third-party authority to tell you what’s safe and what’s not.