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It doesn't seem wise to introduce students to the evaluation of scientific theories using something ideologically charged.

Starting with an ideologically charged example is indeed not a good way to do it. If it were up to me, I would first teach students the general principles (with politically neutral examples to assist them). Then they might be given past examples of how ideological bias could trump science (for instance, the history of genetics in the USSR). Finally, I would let them learn about present controversies (creationism, global warming etc.) by independently reading the arguments of each side.
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