Would you rather read a really bad article that has no JS or a very well written one with JS enabled?
That's not always the choice though. There are lots of good articles, so you could ask: Would you read one good article that requires you run a (non-free) program in your web browser, or would you rather read another good article that doesn't require that? (or simply read the article elsewhere, if possible)
Presumably OP doesn't have an issue with sites that have "JS enabled", but sites that don't work at all without JS. For example Wiki Wiki Web[0] fails to display anything but a spinning loader animation when JS is disabled.
[0]: http://wiki.c2.com/
Although I agree with the issue being sites that don't work at all without JS enabled. (That is why I suggested ignoring JavaScript when indexing.) (The c2 wiki should be made to work without, or at least, to add a <noscript> which links to the raw text, perhaps.)
Yes, even just that would make all the difference.