I had the same problem in my first playthrough. I don't know if you tried it already and if it's going to work (maybe I was just lucky), but after I had cured Farkas I still couldn't get it to activate, even with the heads in my inventory. So I went to Farkas at some point asking him for a random quest, and he gave me some bandit-clearing quest, and before visiting the bandit site and completing it, I went to the tomb first. At that point the Flame of the Harbinger activated, I tossed the head in, fought the wolf spirit and cured myself. At any other time it wouldn't activate, not even when I was on the quest to cure Farkas, but during the random quest it worked. In my second playthrough it worked when I cured Kodlak.