From what I could interpret from the game, Karma and the Heavens are two separate “entities”. The Saint MC can have good Karma, which is why certain techniques don't even work against him, as we can see in the Danger Zone Events; while the Dark Side MC has bad Karma, which is why DES's techniques are extremely effective against the MC. As for the Heavens, it hates the MC regardless of the route. Ruo is an exception, because both the Heavens and Karma love him, so whether he's a Saint or a Demon, Karma-based techniques should have no effect on him.