Definitely, though it'll be very hard to quickly translate 100% of jQuery code to just JS. This is because babel really shines as a syntax transformer (where crystal clear what's intended to happen in source code) vs jQuery which is a runtime library (which it's impossible to handle every case, because you can do crazy things in JS at times).
But if you're looking for something as simple as transforming $.each(array, () => {}) to array.forEach(() => {}, there shouldn't be any issues at all. Try checking out babel-codemod