If it's the latter, can you give some concrete examples? I'm genuinely pretty curious because all my experiences with post-secondary academic history have been unusually non-partisan (compared to many/most other social sciences).
If it's the former...well honestly that's just silly. Just because it's a favorite tactic of the left to claim that anything contrarian is critical thinking doesn't mean the converse is true (i.e. that anything labeled critical thinking is on the hard left).
I find the claim particularly dubious for history: if you really squint and try to label it as partisan, it seems just as likely to me that it would seem right-ish than that it would seem left-ish. The discovery students make in the postsecondary study of history that historiography exists is one of the linchpins of history's alignment with critical thinking: instead of reading sources (and historians) as bearers of incontrovertible truth, you realize that they make up a best-effort account of facts subject to things like lack of information, blind spots, etc. This is fundamentally similar to not blindly trusting academic and scientific authority, a view which dovetails neatly with both the contemporary and historical right[1] (the latter case including opposition to things like high modernism on the left). It's true that a level of distrust of status quo knowledge exists on the left as well (e.g. post-modernism), but that just reinforces my point that it's not fundamentally partisan.
[1] This isn't a commentary on which approach is better, but I hardly think it's controversial that the idea that scientific facts are set hard in stone and you're simply flat wrong if you question them is far more common on the left at the moment than on the right. Skepticism of academia and the scientific establishment consists both of 1) anti-intellectual "scientists are all scammers" and 2) a sober-minded recognition of the limitations of the scientific method and the attendant belief that progress based on scientific knowledge should have some brakes built in.
I'll try to re-state it. In my experience, outside of hard science every one of my professors who was fond the phrase 'critical thinking' was pushing marxism hard, including several history professors I had.
I'm not trying to state that history is hard left overall. Just that if I heard the phrase 'critical thinking' I should prep for a long lecture on worker alienation or class struggle.
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".
I think you probably need to take a few more courses that will help your critical thinking ;)