This is another one of those RMS things which really does seem pretty nitpicky and impractical, at the time it's written but history shows that whenever you later look back, RMS is almost always right.
Javascript is so transient, so unimportant, and so close to the blurry line between code and content (though I'm surprised to be reading so many opinions here which are placing it on the "content" side). Our browsers are getting pretty decent at sandboxing these days, so the consequences of running unmaintainable and unauditable code within them, seem light. Who really needs maintainance for code that you only use for a few seconds and then throw away?
But it's creep. Unless I have my browser only run Javascript from whitelists, the "normal" operation is that it's doing something (running all kind of crazy proprietary stuff) that, outside the browser, just doesn't happen. My machines aren't are "pure" as RMS' machines but even so, there are really only so many places where I still have unmaintainable and unauditable code. The browser multiplies that by thousands.
It's funny; I normally don't go adding thousands of proprietary PPAs to my Ubuntu machine, and tend to be pretty conservative about what I allow to be installed. Yet my browser still isn't using a whitelist for Javascript. That's not entirely sane or consistent, is it? No matter where you stand on the Free vs proprietary spectrum, you get to call me a hypocrite. (Fortunately, I probably get to call you one right back -- unless you're as hardcore as RMS or as resigned as an iPhone user.)
They're individually inconsequential (I think!!), but I sure spend a lot of time in the browser. What's otherwise a fairly trustworthy machine, seems to be hanging by a thread: the browser's correct virtualization of the Javascript universe. If I'm really ok with that, then you'd think I'd also have some Windows or Mac OS X virtual machines around too, to further run more unmaintainable and unaudited code for my convenience. Why don't I? Maybe it's simply because doing that wouldn't really give me any more convenience. But maybe I'm inconsistent because I don't have my shit together, mentally.
I think there's a valid concern here, it's just hard to say it's important or what (if anything) to do about it. But I remember when "The Right to Read" pretty much got the same opinion from me.
As far as what to do about it, FSF's proposal seems pretty modest: don't have government actively making the creep deeper. We have enough to worry about without our own government putting us further at risk. Regulations.gov shouldn't be distributing a bunch of proprietary code to citizens; leave that sort of thing to commercial sites. Even if it's currently believed that the current version of that code is harmless (it wouldn't totally surprise me if some people have illegally(?) audited the Javscript), it's not a best practice, and outside of exceptional-because-we-don't-have-our-shit-together web it's something we normally wouldn't do or permit. If regulations.gov told you to download and execute regulations.exe or the iOS app as the only way for citizens to get some information from them, I'm sure plenty of people would be screaming. This is the same, but also different, by degrees. Whether it's two degrees or ten, though, I don't know...