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I'm saying the letter of recommendation is a teacher's perogative.

Your statement does not in any way excuse the abuse of power by this teacher.

Do you consider it moral to FORCE the teachers to give letter of recommendation to all students?

No, I consider it immoral to deny it to a student who deserves it due to his not agreeing with the teacher's atheistic beliefs. I consider it immoral to essentially force someone to deny their religious beliefs in order to continue their education. This is the essentially the same as forcing someone to deny their faith or die. This is the behavior of petty tyrants and totally immoral people and you should be ashamed of yourself for defending such behavior.

There's no abuse of power. A teacher can refuse to write a letter of recommendation for whatever reason he wants. He is under no obligation, moral or legal, to give a letter to any student he feels is "unworthy", and he is the ONLY applicable judge to the "worthiness" of the candidate. You and I might not agree with his assessment methods, but it's none of our damn business.

Part of the first ammendmant gives people the right to freely associate (or not associate) with shomever they choose. Writing a letter of recommendation is a form of association, if he chooses not to associate himself on this professional level with the student in question that is 100% his perogative. I knew a prof who would only write 1 letter of recommendation per school per year (and he didn't write general letters, they were always addressed to the admissions board and not given to the student to send out willy-nilly), so if you wanted a letter from him and were aiming for a popular school you'd better ask early. I thought that was a pretty stupid policy, but it was his policy, if you didn't like it you went to a different prof.

It's not like this guy is the absolute gatekeeper. Just because he doesn't write a certain student a letter doesn't mean the student has capped out. The student has 4 years to impress profs enough for them to write him a letter, this is only one guy.