Because Javascript is always on by default, someone has to actually go out of their way to turn it off. These people should also know that when they visit a site and something isn't working properly to turn it back on. The only exception to this is mobile device users.
So, unless you've got a lot of people using a mobile device which doesn't support Javascript, the only people you'd be alienating would be those who did it to themselves and know how to solve the problem.
Seems like a non-issue to me.
ps: oh - just don't hide all your content in the Javascript: you still need search engines to find you.
Edit to respond to the comments and downvotes:
If you're building an application, as the OP is talking about, then you should be able to expect that your users can turn off their (paranoid) plugins, so that you can use whatever reasonable technologies let you get the job done. This includes Javascript and Flash. If you're building a site, then definitely build for the lowest common denominator and add progressive enhancement with Javascript and whatnot. There's a very important distinction between an application and a site.
(and yes, i realise i've altered my original argument)