Maybe he would, maybe he wouldn't. There's no way of actually knowing if Jon would have more losses had he fought back then, or if he'd have an even better resume. You have to take into account the fact that he'd be able to juice to his heart's content, so you'd have the best version of Jones every time he stepped into the cage.
Chuck does pose a threat to Jones, but there's no guarantee that he wouldn't have trouble with Jones' range and wrestling. You have to remember that Chuck was very hittable and his opponents usually got the better of him until he turned things around with his power. My guess would be that Jones would fight very defensively, using his kicks and footwork to avoid most of Chuck's strikes, he'd get caught here and there, but I don't think Chuck would be able to seal the deal before getting clinched and thrown.
It wouldn't be a domination one way or another, but I give Jon the edge.