The reason to avoid jQuery while learning is that it teaches you to use javascript lazily as an afterthought to get a DOM element to do what you want quickly. It doesn't encourage you to learn a single thing about javascript.
jQuery is essentially a better DOM API than the native API. Hence it focuses on DOM manipulations, which, despite all we've learned about other important pieces of client-side webapps, is still an important piece itself.
jQuery won't help you much with architecture, but then again, neither will your text editor, and it's about as guilty as your text editor or the native DOM API of helping you learn JS or use it effectively.
I don't know about that! People were writing terrible JavaScript to perform DOM-manipulation magic long before jQuery came around.
I think it has more to do with how people see JavaScript, i.e., whether JavaScript is a general purposes programming language or just a tool to make cool things happen on web pages, than it does what framework they do or don't use.
