Well… the worst thing possible for the Eternal Universe had finally happened. Through unforeseeable circumstances on their part, Dante had identified the backdoor left in his technology and even knew where it led to.
The Eternal Universe originally had a plan to deal with Dante if he ever found out, but that was supposed to be far later. They could never have predicted that not only did he have counterfeit fruits to exchange with the spire as well as the mutation cores, but he would have something like the Nirvana Fire of a Phoenix as well.
It was one thing to trick Dante on their side, as Dante had accepted the deception as fair game and even benefited from it immensely. Not to mention that he would have made the same choice anyway without the deception, so the hatred level was pretty low.