For example Linux, Mac OS X, Windows do control your System by taking over all resources, interrupts, almost anything.
At best this is a Browser Operation System (BOS), and even then it's not - because it does not have control over the Browser.
It's an illusion.
Be that as it may (I haven't fully checked out the source to this thing, so I can't say if it could "operate the system" or not), there's nothing preventing anybody from writing an operating system in (mostly) Javascript. You'd just have to have a JS interpreter built into your kernel. Now, why you'd want to do that other than for pure hack value, I cannot say. Nonetheless, it can be done.
Edit: You could also (theoretically) have a specially microcoded system that can directly run some form of Javascript bytecode, as was done with the old Lisp machines.
It's also open source: