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It's odd, actually. I've been playing through the game again recently and decided to go with James (after finishing it with Charnel; now I'm doing it with Pyro). During the penultimate mission, Gammel died, and since I love the guy, I decided to start over. Next time, Faetus died, but I wasn't too bothered about it--I picked up his souls and all.
Then, when I enter the last battle, there he was again! Is this normal? I don't recall it happening before whenever any of the other hero units died and I went on without them--then again, that hasn't happened a lot for me. And I usually only restart the level if I lose either Gammel or Sirocco, as far as hero units are concerned.