If you remove options from your product that are vitally important to even a small number of users your product can no longer "be used by anyone."
Users with images turned off by someone else wouldn't be confused if there was a yellow stripe across the top of the screen with a "you're viewing this website with images turned off [turn images on]" type message. Same goes for a "this page may display better with javascript enabled. [turn javascript on] if you trust this site" message for those browsing with javascript turned off.
Similarly, as the original post points out, the big issue with SSL is that you get a scary (and inaccurate and incomplete) message telling them to email the website owners because their site is broken, and not a simple message they'll need to "click here to turn SSL secure access back on" to view the web page.
If the developers/designers of Firefox don't have a reasonably answer as to why a large enough amount of users would disable these settings, then they should be removed (or to avoid upsetting existing power user moved to about:config).
If I recall, there are some Chrome options that you can't modify from Chrome itself, but which you can configure using Group Policy Objects. That (or whatever the equivalent is on *nix--files in /etc?) should be where the settings for "lab admins" go.
User interface development for mainstream software is invariably a balance between presenting something accessible to novice/occasional users and presenting something powerful to expert/frequent users. You can go a long way to helping both groups with a thoughtful design, but there's always going to be someone who wants something slightly (or completely) different.
For mainstream software, trying to please everyone all the time is a fool's game. That's what bespoke development is for.
Same argument can be said for removing a feature 2% of the population of users rely on. 2% of 450 million users is 9 million users. Not what I'd call a tiny number of users.