Who was the new priest?

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Fonda is indeed a kind of Christ, but maybe even more Crist and St Peter in one person. Fear, doubts, insecurity that Fonda's character shows and especially his running away remind on St Peter (don't fugitive's hiding when people have been arrested, and running from the country correspond with Peter's denial?). Also, the priest needs wine for a sacrament, but (unlike Jesus) he can't transform water into it (so he disappoints and betrays those who believed him, what Christ never did). However, at the end of the movie the fugitive priest does look more and more like Christ, his talking with doctor can be compared to Jesus on Mount of Olives before he was arrested (but in a way that we could imagine Kazantzakis' Jesus to do it). The lieutenant is Pontius Pilate, his conversation with priest in the evening before execution leaves no doubt, he understands and to certain level admires his prisoner, but is too firmly bond to the other side to find strength and courage to change. Of course, it's fun to look for other relations, the police informer is Judas Iscariot, Maria Dolores is a kind of Maria Magdalene, the Governor may be Caiaphas etc.

Now, back to father Serra. We can explain his appearance in two very different ways. First, he could not exist at all, it was a metaphor of peasants' faith, either a hallucination or a materialisation of faith. Second, if he is real, as (unlike Christ from Testaments) the fugitive priest had no pupils, he must be someone newly converted to Christianity. If we look into the Bible again, the only character that would match would be St Paul, former opponent of Christ who was prosecuting his pupils like army and police in movie prosecuted priests, but then changed into one of the Apostles.