Actually none of the villains were killed. Nightmare Moon was turned good again and Discord was encased in stone. Both have a chance to have future appearences, though less of a chance than the changelings, and Discord more so than Nightmare Moon. I've also heared that John DeLancie, Voice of Discord, is returning to the show, though I'm not sre if it's true.
maybe, but the writters could do anything they want with their show. like they could make it so that somebody made a second Nightmare Moon, or if somebody somehow releases discord. villains always come back in TV shows even if they were actually "killed".