He just doesn't want this GNU project to include support for a language whose primary purpose seems to be invading privacy -- even if it has a lot of great secondary purposes and a good open source ecosystem. Given that the GNU/FSF projects are all about advocacy in the area of software freedom and privacy, it seems like a reasonable perspective to have. Yeah, RMS definitely takes things to an extreme, but I don't see the "JS is implicitly evil" thing you're calling out, just refusing to appear to endorse or support something that goes against his principles.
And of course ironically enough those very principles mean he (should be...) perfectly happy with the emacs-ng fork, since that's part of the freedom he's advocating for.