At my last startup Outspokes, our product was an embeddable JS-widget. While we did load jQuery after initializing the widget, we still used basic Javascript to load the initial widget (think bookmarklet-like code). Because so much of our app was written in JS, we put more effort into structuring models and creating tests for our widget. This was pre-backbone days, so we built out a set of conventions for ourselves.

I agree that jQuery is almost like a superset of JS, and it hides a lot of the nastiness of some day-to-day chores. But it's still good to understand the underlying JS that powers jQuery.