Someone else was saying, not me though, that you can cure it right after the point where they turned you into a wolf by becoming a vampire. And that the story would still continue, but for whatever reason he could not get the side quests to cure any of the other companions at the end.
I believe in order to start the cure quest you need to have the witch heads with you in your inventory for a couple of days before they ask to be cured.
I'm not sure, I just have the witch heads stashed in a chest in my home but I can try and see what happens. It's not real big deal to me and I don't really have interest in the totems since I don't plan on playing a werewolf on this toon. However the main quest line was finished as a vampire, starting from the point right after I got infected with lycanthropy, I turned right back into VL. Apparently the companions aren't scripted to care. The only part is that when you speak to Aela, you have the option to turn back into one, but only once. Otherwise no one gives you flak unlike the vampires in Castle Volkihar.
One thing I am interested in testing is seeing if I can cure Vilkas (my husband) of lycanthropy and turn him into a vampire with one of the side quests from Vingalmo.