The author of that article says: "Is it really worth having a preference panel that benefits fewer than 2% of users overall? — obvious spoiler alert: The answer is no."
The answer is yes. If 2% of users have a purpose for it, perhaps it wouldn't have been high up on the priority list to implement as a new feature, but it's already there, and removing it requires extra work. Is it really worth removing features from an application to deal with some hypothetical problem that's been posited under the assumption that most users are idiots?
If there really is a problem, it may be worthwhile to move it to an "advanced settings" panel, but removing it entirely is a terrible idea.
It's worth noting that Chrome - a browser that's far less configurable and customizable than Firefox, overall - not only offers the ability to disable JavaScript globally, but has it as an option in the domain-specific permissions menu.