[Aiwendil]

. For example, when movie critics censure a movie based on poor plot or bad acting, people may disagree, but they aren’t going to say that plot or acting have nothing to do with making a movie good or bad.

I think we need to be a little more clear about definitions. When movie critics express their opinions on a movie, they are not in any way preventing people from having access to the movie. I don't think that anyone has condemned the expression of opinion with regard to an idea; what is being discussed is the act of preventing other people from access to that idea.

But if an authority in an organized religion where to say to its believers that such a book or movie is bad based on doctrinal or moral reasons, people come out of the woodwork to say its “Censorship, and all censorship is wrong”

Perhaps some people would, but certainly not I. There is nothing wrong with expressing an opinion, even if the opinion is incorrect. There is everything wrong with enforcing your opinion on others (that is, through force rather than through argument).

I found much more close-minded people in the public school system than I found in the Catholic parochial system.

I cannot dispute your own account; however, I know at least one person who attended Catholic school and has formed exactly the opposite opinion. The difference may be this: that he is not Catholic. Which is exactly what my point is - if you're Catholic, of course you will not find much fault in the teachings of a Catholic school; if you are not Catholic, you may. Thus, Catholic schools cater to Catholic interests. Of course, I don't know whether you are Catholic.

At least in the Catholic schools there was greater freedom to broach controversial issues dealing with God, morality, religion, etc… because the school, parents, and teachers weren’t threatened by these controversial issues due to their firm acceptance of the Catholic Weltanchaung.

Still, you can't deny (at least, I don't believe you can) that Catholic schools teach Catholicism. If a student therein were to ask a teacher if there is a God, what would the answer be? Would it be "I don't know?" Because that is the open-minded answer.

In the public schools, however, there was considerable worry that any discussion of any religion would offend an administrator, parent, or teacher; thus all religions were investigated in only the most superficial manner.

I'm not sure how true this is of most public schools. Insofar as it is true, it is very unfortunate. I am not advocating this kind of closed-mindedness. In fact, what you just described is a form of the very censorship I am attacking. The point is that public schools should be a place where ideas of diverse kinds are tolerated.

Incidentally, my experience in public school was not at all like what you described. We studied the teachings of Christianity, Judaism, and Islam; and we discussed the role of the church in ancient and medieval Europe as well as in the Renaissance and modernity.

Attempting to discuss medieval Europe without mentioning the Church is like trying to teach geometry without mentioning angles.

Indeed; and it is a form of censorship.

in regard to morality (as opposed to ethics)

How do you define the difference between those terms? In my usage, they are synonymous.

Should toleration be upheld at the expense of one’s faith?

Short answer: yes.
Long answer: Any imposition of one's own faith upon another person is an act of repression and is immoral. Suppose members of some faith demanded that the Bible be banned in order to prevent the spread of falsehoods. Should they have their way? Of course not. Nor should Christians who ban Tolkien (or anyone else).

In this case you are either to oblige these people, and, therefore, pull all fantasy books off of public library shelves so as not to offend them, or to present a staunch argument against their principles, and thus save those fantasy books from banning.

One need not argue against the all the person's principles. The only principle incompatible with freedom to read any book one wants is the principle that one's own beliefs should be imposed on others. It is possible to be tolerant both of a religion and of ideas that contradict that religion.