For Stallman and the FSF, it's not (just) about the practical dangers of unknown software running about your machine; it's about the moral right to modify and reuse that software.
Even taking that pursuit as a given, I still don't follow the point of this. 99% of the JavaScript I use is intimately bound up with server-side software that I don't have access to. What's the practical value in having half a free app running in my browser when it's useless without the proprietary half on the server?
They is why they also criticize the trend for closed and unaccountable server-side applications (in other publications / articles). The evolution of the GPL is supposed to go in the direction of fighting this trend (although it's very difficult, for a number of reasons).
Stallman and the FSF are not everyone's cup of tea, but they are extremely coherent about their philosophy. They (over)think about how we interact with technology, lay it bare for everyone else to see, and then propose alternative ways. Not everything Stallman says or does can be practiced in everyday life (among others, he runs a Chinese-made laptop that only contains hardware that is fully documented, and spends quite a lot of time sleeping on other people's sofas as he travels around the world to spread his FSF gospel), but it's usually impossible to attack his position on purely-rational grounds.
