At the end, Marta and Thomas both engage in rituals; but Thomas goes through the motions of a ritual he does day in, day out, without variation, for the public benefit only. Marta's ritual is private, personal, and because she never does it, none of its spiritual content and value has been rubbed out by habit.
You see this. I see two people in prayer together
I just rewatched the end of the movie (which I had misremembered slightly--I thought Marta bowed her head in silent prayer while Thomas began to read out the service), and there's this moment, when the bell signalling communion begins to ring, where Marta suddenly gets to her knees and asks "if only we could feel safe, and dare to show each other tenderness. If only we could have some truth to believe in...if only we could believe
." The 'prayer' is shot as a close up of her right profile, and in the midst of it Bergman cuts to a shot of Thomas with his eyes closed that matches the framing of Marta's face as her voice plays over the image. They appear to be connected in the same questioning of our capacity for genuine feeling at this moment, so Bergman does seem to be suggesting what you say above. Although perhaps the prayer is directed at Thomas
rather than herself, and the cut connects her words to his predicament and signals their true subject, instead of being put into Thomas' mind. It would make sense: she has just been tempted by the organist into giving up (the organist standing in, I suppose, for Job's neighbours, who tempt him to despair), so her reaction to pray and to ask about the very things Thomas obviously lacks, and which she has been trying to cultivate in him, also suggests, as does her choice to stay for service rather than leave, that she
rather than Thomas has passed the test, has retained her capacity for fellow feeling.
Anyway, the prayer precedes the service (the latter is not a prayer anyway), and the service becomes a chilling irony when Thomas repeats the words: "Holy, Holy, Holy is the lord of Ghosts. The whole Earth is full of His glory." The words of the service clash against the words we just heard from Marta, and become emptied of meaning because of it.
As you suggest, this as well as other scenes you mention precede the character's turning point with Algot. It's always darkest just before the dawn...
Perhaps. Algot's point is that Christ's physical sufferings were nothing compared to the anguish of doubt, of feeling alone, of being confronted with God's silence (he speaks of Christ's moment of doubt on the cross). He ends on that note, and Thomas, with an agonized face, replies "yes." Has Algot given him a crucial epiphany, or has he even more brutally reinforced what Thomas already fears most: being empty and alone? It seems like the latter.
So, having pushed away Marta, having been told feeling abandoned is indeed the worst of all possible sufferings, and having asked God if human connection and fellow feeling is at all possible, the confrontation of an empty, silent church with the hollow words of God's glory on his tongue...I don't know, I'm not feeling it. Especially since Bergman does not include Thomas and Marta in the same shot during the service, and doesn't match their eyelines in the cut from her to Thomas beginning the ceremony.
It might be optimistic, it might not, but I still side with Marta at the end: she's the only one trying to really make connections throughout the film, the only one not giving in to despair or bile, and tho' Bergman collocates their faces during her prayer, it is her words that we hear vocalized, not Thomas'. I think you're overstating the spiritual connection between the two of them at the end. If there is any hope for Thomas, it is because of Marta's continued humanity rather than a spiritual epiphany on his part.