Reading Das Kapital should be an exercise in critical thinking, regardless of one's political persuasion. For example, where in the software industry is the labor theory of value a reasonable model? Where is it not reasonable? Why? Answering these questions requires what any reasonable person would call critical thinking.
Conversely, hearing a bunch of passionate lectures about worker's rights movements is considerably less enlightening...
That's probably true.
> For the professor to present the arguments anti-Marx in his class would in fact be just the opposite: capitalist indoctrination, where you would be lead to believe that Marx was really wrong and capitalism is the only "correct" system.
Also probably true.
The problem, though, is that the professor is only presenting the Marx side, while claiming to teach critical thinking. That's not critical thinking! Critical thinking means criticizing both sides.
Now, if the professor wanted to teach the Marx side "as a balance to what everybody else says", that's OK too. The problem is the one-side-only combined with the claim of "critical thinking".