Due to the names Java and JavaScript being so similar, users get confused when their technically-minded friend recommends that they disable Java in their browser. Somewhat like ham and hamster, with no prior knowledge the user has no idea that the technologies are entirely different.
I've personally had to help a number of people out who have mistakenly disabled JavaScript. That was the impression I got.
The current trend in removing features from software seems like a great way to have a dire shortage of engineers in 50 years time. The attitude that "software is a magic and untouchable black box, you can only use it to do the specific thing the developer wants you to" destroys the true power of the computer as a tool, it might as well be a radio or a TV that incessantly produces other peoples ideas.
Write useful, empowering and well tested modular code. Let the user work out what crazy and wonderful ways they arrange those modules. Don't make changes that serve only to glob more functionality up in to impenetrable, monolithic black boxes. </proselytizing>
Also: Overriding peoples existing preferences during upgrade? Nice work guys :/
They don't want to be 'empowered' by developers, and they definitely don't want to have to deal with arranging a bunch of poorly documented modules that make no sense if you are not familiar with the underlying architecture.
Evidently the firefox developers do not think there is a very good reason for disabling javascript to be in the general options, so they removed it.
http://www.amazon.com/The-Paradox-Choice-More-Less/dp/006000...
As a person who uses noscript every day in FF, at first I thought this was a bad idea, but the more I think about the support aspect of this, the only time I think you really should turn off JS is when you understand enough to find the advanced options.
I hate javascript with a fiery passion. But I'm sensitive to (possibly real) arguments that people are accidentally disabling it because they start clicking random stuff in the 'content' tab of preferences. So move it to 'advanced' and call it a day.