Misawa is basically telling him, “Judai, I know you feel terrible about killing all of those people because of you powers, but you need to go back to using them because you are the Supreme King, he’s not some other entity, you’re the same person. And we need your powers if we’re going to get out of this mess.” And I can see why Judai’s so afraid of these powers because of what he did with them before. Like, why would you want to go back to being a homicidal maniac? (I know that’s not what Misawa is implying, but that’s how Judai interprets it.) It sounds like the Supreme King’s powers are hard to control due to some of it stemming from his anger. He must also be fearful that he could lose control and go berserk once more.

Dark powers do not sound like a good thing either, but Judai seems to have completely forgotten about what Aqua Dolphin told him back in episode 62 on his powers of darkness being a force of good and righteousness. Judai probably forgot about them given that he barely used his dark powers when he fought against Saiou.