Late response here... but I feel that showing impending doom in the next season would be a good way to go. I mean, we all know the way the whole thing ends. Personally, I feel it would be best to kill off Ashoka, but have a couple ways it could be done:
1) It happens sometime before ROTS in the general timeframe, her death results from something that Anakin feels he could have prevented, and through his sadness for Tano's loss, he gets pulled closer to the dark side. (I see this as somehow being the most likely scenario).
2) Tano survives up to the general ROTS timeframe and the last couple of episodes take place while the events in ROTS unfold, but offer us a different view of what was going on elsewhere besides Coruscant, Utapau, and Mustafar. After some brave and very intense fight scenes, she gets whacked by the clones during the Order 66 purge. Ideally, it would be Captain Rex that would shoot her, just to hit home the tragedy and make all those clone-loving pre-teen viewers cry