If JS, absolutely needed JQuery in order to, say, select an element the way C needs a library to output to the console, then sure, you may have an argument here.
Because literally any child can start developing, and then grows up and pulls every library under the sun because the language they use is a piece of crap, without a single thought about the consequences?
Thankfully node.js is bringing this clusterfuck to the desktop too.
It's more about deployment and dependency problems.
The dependencies we are talking about are transparent to the user, save only for some download performance issues which are pretty minimal, if not overstated in many cases, compared to the former issues faced by native applications.