For the most part, I would expect jQuery to work the same way that it does in Safari. This is not to say that you won't find interesting bugs and edge cases where jQuery does the wrong thing, of course. If you find such problems, file bugs with jQuery, and if they conclude it's a bug in iBooks, then file bugs against iBooks.
But yes, you
almost certainly will have to embed the jQuery library code in the book. To the best of my knowledge, EPUB books are not allowed to use resources outside the book bundle; they must be self-contained.