This has happened before. A series gets cancelled, but scripts end up getting translated into a different medium. As far back as Star Trek the Original Series, many of which became the animated series, and Joss Whedon developing the final season of Buffy for a comic; the stories find a way to get told. Dark Horse Comics, who will end its long relationship with Star Wars, is going to give the fans of Star Wars: The Clone Wars one last hurrah. Newsarama.com had an exclusive story/ interview which revealed their plans to tell at least one arc of The Clone Wars series. Yes, there will still be the Bonus Content/ Lost Mission that Disney has promised. Yet there were still many story arcs to finish. As you have probably guessed by now, Dark Horse will tell the tale of Darth Maul in Darth Maul: Son of Dathomir (a 4 issue mini-series). That story will be told by Jeremy Barlow (Boba Fett: Overkill), though the artist has yet to be announced.
As a fan of Star Wars: The Clone Wars I am looking forward to finding out exactly what Darth Sidious had in mind for his ex-apprentice.
Read the full interview with Jeremy Barlow here on Newsarama where he discusses the mini-series.