I think Sidious should turn her to the Dark Side, forcing Anakin to kill her. It wouldn't be hard to turn her. And Anakin killling her would send him further down the path to darkness.
And him killing her would explain why she isn't mentioned in ROTS. You know how he doesn't like to talk about the bad things he's done.
Well if you remember..in, I believe it was, season four..Ahsoka has a vision of her future self...who warns her that she might never see her future if she continues to stay by Anakin's side. So I think its safe to say that the creators and writers of the show have something in mind to explain why there is no mention of her in ROTS.