So, you need to make sure you complete her quest line (Fight her at the shed once Billy comes to you and talks to you about it - This happens on Day 5. Then, you'll fight her a few days later outside of the lab and then a final time just before you enter the castle. If you complete all this, after beating the Queen, Isabelle will show up again and challenge you. Once you beat her, you can ask her to join you. )
Hope this helps!