Students should challenge a professor, absolutely, but typically they should not challenge the professor on the basis that they do not agree that something should be taught. For example, if a professor adopts a rat-choice frame, then a student with a more critical approach might critique the use of rat-choice, and rat-choice's weaknesses as an approach. Of course it's pretty unlikely the student has the theoretical grounding to do that. But yes, hypothetically, challenging that is not a problem. But if it's a research methods class and a student says "I don't agree with rational choice so you shouldn't teach it", that's simply disruptive. Whether you agree with Marx or not, agree with Durkheim or not, agree with radical feminism or not, agree with realist IR or not--these are all things that are important to teach an awareness of in the subjects in question. You don't get to opt out of a question on Marx's reification in a classical social theory because you think communism is bullshit. You don't get to opt out of a question on US Cold War FP doctrine because you don't like America. You don't get to opt out of a question on how religious groups have shaped public policy on HIV because you agree that HIV is a punishment from God.
I agree that students shouldn't write value-based criticisms of ideas, parties etc but I think you're being a bit one-sided against students complaining (I don't endorse the complaints of the three white kids, I would have to take that course myself to know if she talked about structural racism too much).
Like you I did political science at university. There was one dreadful course, International Political Economy, that was taught by a Marxist professor (I'm not exaggerating, she wasn't moderately left wing). There were three main theoretical approaches described in the course guide, liberal, realist and critical (aka Marxist) as well as a couple of lectures covering minor things like feminist contributions to this field. The professor spent far more time on the critical approach than the other two main views put together, and even a pretty left-wing guy on my course was complaining that we weren't seeing more of the liberal approach.
If anyone had complained to her about it, she could have used your argument there- we were undergrads and unfortunately weren't in a position to tell how much of each she should teach. She could have said that most of the literature (or at least major literature) was being taught in the course and as it happens, it is critical theory is dominant at the moment. If we complained, 'why do we have to hear so much about the Marxist interpretations', I think we would have been correct to do so. As it happens I disagree with it, but she really was teaching it too much.
So in short...
In all cases, a student saying "I don't think the course should focus on the thing it's focusing on" makes an assumption that the student should direct and tailor their own learning, rather than that an arts education ought to round a student out by exposing them to major themes and perspectives.
Your own assumption doesn't allow the possibility that professors themselves might focus on one theme/perspective too much- the course description might cover many but in practice it is biased. In IPE we were supposed to get a balanced view of the major themes but we didn't.