I love the Jonah and the whale story. There is much to learn from it. Yes, Jonah acted in his free will. But he still didn't want to go to Nineveh. He hated those people and was not happy about God saving them.
Going to Nineveh was just a better alternative than whatever else God would do to him if he didn't go. And that's often how God will get us to do what he desires us to do. He'll make it to where disobedience is much more painful than obedience and so we make the right choice then, in our free will, to avoid pain.
But that happens mostly when we are in immature states. As we mature in him, and grow to love him more, our wills start to line up much more with his will, so that we just want to obey because we just want to, not because there is a painful consequence if we don't.