I like seeing TOS era stories here and hope to see more from you. Spock--and Vulcans in general--can be difficult to write. It can hard to catch the subtlety that's required in showing such things as love, comradeship, compassion, and so on. I can see that you've put a lot of time and effort into this story and it shows. Also, don't worry about having characters of faith in your stories. Remember the interrupted wedding scene in the chapel at the beginning of "Balance of Terror" where the bride kneels. While, for the most part, the dominant view in the Federation might well be what I like to call scientific rationalism or agnosticism, one of the primary tenets of the Federation is that freedom of conscience for all beings is a right. That pretty much recognizes the existence of religion. Also, Judaism has been around for about 4000 years (give or take), Christianity for over 2000, Buddhism for over 2500, Hinduism for about 4000, and Islam for about 1500 years--they're not going to go away in just 300 years or so.
I hope we'll see you write more TOS stories--maybe taking place on another Connie like Potemkin or Yorktown or just make up the name for a new one commissioned and take them on many interesting and fun adventures in the TOS era.