After having to "blow it all away and start again" a few times myself, I now use Jekyll via Docker. Jekyll themselves take care of all the dependencies and my machine can stay clean.
That's true, but if you're a relatively seasoned developer, the ecosystem is stable enough that you can manage. By "stable", I mean, being able to run homebrew and install something like rbenv. I can't remember the last time Jekyll up and failed on me, but for other projects, it's straightforward to blow away a Ruby install and start clean.
Admittedly, I'm not sure how easy it is to find canonical Ruby management tutorials when starting out. I think Ruby's system is somewhat simpler than npm, but only because I don't do too much with Ruby and don't often need to change things around.
I tend to blow it all away and start again in this situation, when I've got time I intend to move away from Jekyll