Well, being offed via a plot from Dooku would be a fitting end. That would explain some of Anakin's hatred on Dooku.
Well, getting her exiled would be good also, not only is it a better plot, that would explain the lack of her being mentioned in other articles. Preferably she should be leaving on bad terms. Hence, she is not mentioned. No, none of those going darkside crab. That would be all too standard. But yeah going AWOL on her own away from the order might work.
Its probably NOT:
1) some great Heroic death, or it would be hard to explain why she is not mentioned.
2) killed by order 66, since that would actually draw Anakin away from his decision on joining Palypy if anything.
3) Die saving Anakin. cliche, plus it would be something emntioned by Anakin every now and then.
4) Die "pulling an Ankin" style action. Then its all Anakin's fault.
Remember There are only a few that Anakin is really attached too, his mom (Dead), Padme ('duh), Asoka, ObiWan.