It depends on the project's complexity, and also on how many generations of developers have dogpiled horrible kludges onto the original code base.

For simple apps, it doesn't matter much. Do what gets you in front of users soonest.

For more complex apps with a lot of client-side state, you may quickly find yourself outside of jQuery's intended use case. Note that simple apps often become much more complex under ongoing development.

What creates problems is trying to pile on a lot of questionable commits without enough structure or organization, and trying to shoehorn it into use cases which it's really not appropriate for. In practice, these situations occur much more often than people anticipate.