It is probably easier to list the things that _won't_ put off RMS.
God forbid you use the DOM[1] in your JS!
God forbid you use the DOM[1] in your JS!
Stallman's position is that the principles of Free Software apply to non-trivial JavaScript code. That seems reasonable enough. His definition of non-trivial JavaScript is such that any JavaScript that modifies the DOM, is necessarily considered non-trivial. Again, seems reasonable enough.
If we want an example of RMS being unreasonable, we need only look as far as the Q&A after one of his talks, where he can generally be relied on to bitterly snap at an audience member for some inexact use of terminology, rather than gently clarifying before answering.
That said, you are quoting out of context, altering DOM makes JS nontrivial. A nontrivial JS should have its source code plainly visible. That was the gist of the article.