According to UESP, if Aela is your wife while you try to claim Whiterun for the Stormcloaks, she may disappear. This is precisely what happened to me. I've tried using the console to bring her to me and it works, but if I tell her to come with me she immediately runs back to Jorrvaskr and stays there, and if I tell her that "it's time to part ways" she just disappears.
Is there anything I can do about this?