This felt oddly like a series finale to me... I really hope we don't get the "Clone Wars is on indefinite hiatus so that everyone at Lucasfilm/Disney can focus on 7,8,9 etc." I know movies are the real moneymakers where the TV series' get brushed under the rug.
Season 6 is already in production. It has its own production crew that wouldn't be involved with the movies, so there's no reason one would have to be suspended to allow the other.
Besides, tie-in cartoons help promote movies. That's why we have animated series based on Batman and the Avengers and Spider-Man and Green Lantern and the Transformers and so on. They're complements, not rivals.