You're overstating the risks a bit and it's not great to posit implausible motives and means for bad outcomes... Like, Fossil devs could "turn evil", and ship an update that destroys your museum and any copies it can find. Github could "turn evil" without notice, and permanently nuke all of someone or some org's accounts for no good reason and yes, that'd catch a lot of people with their pants down. It's better to first focus on outcomes, not means. Of course anyone actually concerned about losing their github issue data (or having their museums corrupted) should at least be making backups. (And it's not exactly an implausible outcome on its own, you can think of a variety of means that achieve it and discover one may be rather more likely for your situation, like if I was a Russian in Russia right now I'd have already made arrangements in case GH changes their mind or is legally forced to drop the ban hammer.)

The desire to move off github (and therefore any additional services besides hosting you were using, which issues are just one -- new ones keep getting added to try and cement your dependence) is something more worthwhile of thought than the idea of github turning evil. Fortunately that desire is an actual thing that's very common, or at least the desire to not be wholly dependent, and is why many people don't even use github issues to begin with even if they use github itself for hosting (or some other non-issues features). So there's not a big problem, and even if you start with using github issues, there are various migration tools to move github issues out to [alternative]. (And of course github issues have their own merits, people frequently want to switch to them! So similar migration tools exist to move from [alternative] to github issues, I wrote one for Jira years ago.)

It is brilliant to integrate things with the decentralized source control itself, you get free backups and deciding to migrate to something different in the future is easy, I think it's an overlooked approach for a lot of people. (It seems less overlooked when it comes to documentation in various forms like developer-focused .md files, or broader full static html websites which github can conveniently host for you.) Fossil is well-worth investigating for this free integration to see if it meets one's needs. But of course nothing stops you from doing it with git yourself in various ways. For personal projects, I'm pretty satisfied with being as minimal as having an issues.md file and moving things to an issues-closed.md file when I close one. I've also used the git-issue extension (https://github.com/dspinellis/git-issue -- see also its bottom section of Related Work).

But despite its brilliance it's not always the right approach. It's very easy and reasonable to want more than what is realistic for something deeply integrated with the source code itself to provide, if only for inherent conflicts of desire, let alone any question of manpower. There are very good reasons to have entirely separate (and even multiple-of-kind partially overlapping/integrating/cross-referencing) systems for source code management, issue tracking, code review, forums, IM communication, wikis, public websites, docs (of whatever kinds and types for various audiences and authors, or public or not, or team-level spikes or plannings or retrospectives)... One aspect of Fossil I found weak was its user capabilities (https://fossil-scm.org/home/doc/trunk/www/caps/ -- no custom user categories alone is a deal breaker for so many things) but flaws in the execution of a fully integrated thing isn't really my point, my point here again is just that full integration despite its overlooked benefits and brilliance when applied to certain things is still not necessarily the right choice for something.