The Horde will remain oppressing Etheria until Prince Zed becomes the new Horde Prime
The reason Adora wasn't entirely evil when she was with the Horde...
...was because Shakra (her nanny, who appeared in a couple of episodes) has secretly taught her about good versus evil, and all of the positive things about good. On the other hand, it's likely that Shakra was simply unable to help her escape the Horde, for whatever reason.note Loo-Kee was able to avoid the Timestopper's power due to the nature of his magic, not simply because he was magic.
Loo-Kee's magic is meant to conceal him, hence his species' name, and can work on a passive level. When the Timestopper activated, it caught most of the good magic users completely off gaurd before their own defenses could stop it. But Loo-Kee was naturally overlooked thanks to his innate defenses, probably helped by being asleep as well, which allowed him to play Spanner in the Works. When Orko travels to Etheria too, he's already prepared to counter the machine's effects, and of course when the Twins hold their swords in their empowered forms, they're immune.