Strongly disagree. You're conflating 2 different things - education and dogma.
Higher education is still education. Your post is like saying that because a college expects a math major to demonstrate skilled used of calculus before they let him/her delve into more abstract and innovative areas of math, the college is dogmatic. Hardly. The student is expected to demonstrate a core grasp of the curriculum of their major...including the "why's". But demonstrating a grasp of material does not equate to being forced to agree with it once the class is finished.
This is why the critiques of critical thinking related to colleges and higher education often demonstrate a problem with understanding education, not a problem with the colleges or with critical thinking.
I'll go anecdotal for a moment. In law school, we're expected to learn certain cases. Specifically, to understand why those cases were decided the way that they were decided. On the exams, we're expected to be able to coherently explain the reasoning that the judges of the time applied to those cases and how it fits within the larger jurisprudence of US law. But we're not expected to agree with the reasoning. We're allowed to disagree with a ruling while holding on the knowledge that it is the law of the land and will control what happens in the real world...whether we agree or not.
To make the law school analogy: What too many people are saying is that if you don't agree with the ruling or you question it, the law school shouldn't teach it to you or expect you to understand why it exists. That teaching any case with a controversial outcome is dogma. And that expecting students to apply the reasoning of those cases is "indoctrination". Those people don't understand education or critical thinking.
As they say "You must first understand the rules before you can learn how to break them." College education teaches the "rules", for lack of a better term. Students learn the "rules". But the students are free to abandon those rules once they leave the classroom. Once they've demonstrated, via exams, papers, etc. that they understood the rules that they are questioning. Learning the how and why behind the rules is the foundation for learning how to critically think about those rules and thus draw a conclusion, after the course is finished, on whether or not one supports them.
People want to skip the education part and just straight to the disagreement part. That's not teaching critical thinking. People should understand the process of training people to think critically about something, as opposed to simply disagreeing with it.