I agree with you that her involvement with Perrin's arc doesn't quite add up, and was likely an addition by Brandon due to the split.
Anyway, her plan for Perrin was very uncharacteristic of her.

I think, as you said, that Graendal would have been captured as soon as Aran'gar died. But I don't think she'll be killed. She'll probably be mindtrapped, or, like Mesaana, humbled and brought under control, but I don't think the Shadow is in a position to kill off powerful pawns now. This would have meant an end to Granedal's private scheming. But I just don't think they can afford to waste her strength and knowledge. Plus, as another of the Foresaken who has it for one of the wondergirls, she can be used to provide the tension of a battle in the next book.

That will be her final role, I think.