Note: These issues are mostly resolved in the latest Firefox.
I hadn’t thought about this before reading this short piece – http://limi.net/checkboxes-that-kill/, but early 2013 Firefox did indeed allow you to break the browser (for non-technical users) just by trying out a few options. I’m sure the Mozilla folks don’t intend for Firefox to be an experts-only tool.
There are several approaches to this issue, but it’s not solvable in a general sense. As a developer, you have to balance usability and configurability and a browser is such a general purpose tool that there’s no way to optimize it for all users.
I checked my latest version of Firefox and most of the gotchas listed in this article have been fixed. The only thing I might add, other than warnings before applying selected changes, is a single button in the main (always accessible) menu that allows a user to reset Firefox to a known-good state, possibly the initial install state without any customizations or addons active.
What do you think?