My current thinking on this is that the show will end with Ashoka no longer being a Padawan and going off with her own troops. They are NEVER going to show her dying on the show. Captain Rex will offer to keep an eye on her for Anakin and ask to transfer to Ashoka's squad as their commander. Then when GL finally releases ROTS on BR, we'll get a new Order 66 scene where Ashoka is taken out by Captain Rex wearing the ROTS style armor - which after the cartoon being on for three or four seasons would make that scene incredibly powerful.
That sounds great. I'm going to be really disappointed if this isn't what happens now. The Order 66 scene(s) are so powerful already and that would just top it off.