My comment actually comes from lots of speaking to end users. I cut my teeth on help desk and desktop support roles; understanding end-user needs is baked pretty damn hard into my blood.
And from those discussions, and from my observations of those users, 99% of the problems discussed would be resolved if it was clear what options actually did. Users don't know or care what "Javascript" or "TLS" are, but you can bet your ass that if the relevant checkboxes had at least a basic explanation of why they should be checked (i.e. "Don't uncheck this box unless you know what you are doing; doing so will cause a lot of websites to break"), the vast majority of end-users will happily leave that box unchecked until they ask someone more knowledgable about it.
But in this case, we're dealing with users who somehow managed to disable JS, but are still surprised by the effects and don't read prompts.
I'm pretty sure such users exist, however instead of directly basing your UI descisions on this scenario, why not trying to investigate where such behavior comes from and how frequent it is?
Imagine a user whose internet isn't working. They go into their web browser's Preferences and start fiddling with things at random "until it works again" (for entirely unrelated reasons.) Then they leave things however they just made them.
And from those discussions, and from my observations of those users, 99% of the problems discussed would be resolved if it was clear what options actually did. Users don't know or care what "Javascript" or "TLS" are, but you can bet your ass that if the relevant checkboxes had at least a basic explanation of why they should be checked (i.e. "Don't uncheck this box unless you know what you are doing; doing so will cause a lot of websites to break"), the vast majority of end-users will happily leave that box unchecked until they ask someone more knowledgable about it.