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I've read that が is the particle used when asking a question, but then I see sentences like 一番好きな本はなんですか or 一番いい先生はだれですか.
Is there a reason why が is not used in this type of sentence, or is the rule re: が in a question sentence just a vague guideline?
I think you have misunderstood the advice you were given. It is not true that が must be used in questions or that は cannot be. But because interrogative words like なに, だれ, etc. refer to undefined objects, it does not make sense to use the topic particle は with them. So if they are the subject of the sentence, then they must be marked with が rather than は. I believe this is all they were trying to get at.
For example:
× だれは電球を発明したの。
○ だれが電球を発明したの。
The question can, however, be rephrased as
電球を発明したのはだれ
without any problem.
