Two things come to mind for me on this topic.
1.) Where do scientist get their training and what is the current state of affairs of free speech in those settings? I think that does go along way to explain the lack of tolerance for questioning the prevailing consensus on any subject. Post-modernism is not in favor of facts or any object truths; it pooh-poohs the very notion that those things exist outside of a subjective perception. It is not going to teach respect for them. Reason and open scientific enquiry become a casualty of that.
2.) Leftism, Progressivism (whatever you want to call it) demands lockstep adherence of everything -- even the Boy Scouts and football. Why would science be any different? And why would scientists be any different than anybody else in fearing the wrath and damage to reputation that could be brought to bear upon someone who asks a question when they are really not so sure of the answer -- i.e. just enquiring?

I don't have the answer, but here are some thoughts on it.

I think you hit on a real point with separation of church and state. At some point during the 20th century, or maybe even the late 19th, science and religion split into two separate coins rather then being two sides of the same coin. Up until this point, most science was done by or funded by the church, right?

Then this split, for lack of a better term, happens, and what we begin to see is science v religion. You start to see this mindset on both sides that both can not be true at the same time. Then I think an all out war ensues.

In war you use every tool at your disposal to achieve victory and the fighting can get quite vicious. I think we are seeing the effects of this war today.

Lately it has seemed that science is winning to some extent, if not by numbers then by having the ability or freedom to manipulate the state to it's agenda. It's a built in advantage they have because the constitution does not allow religion to be the basis of laws, so to speak. There is no such thing as separation of science and state.

However, the pendulum may be starting to swing the other direction. As science digs deeper and deeper into things like quantum mechanics and DNA, it becomes more and more apparent that intelligent design may actually be a real scientific possibility. I think this scares a lot of scientists, and this fear is causing some of the erratic and dogmatic behavior we see now.

Rem acu tetigisti

Pope Benedict XVI basically provides a discussion of #3 from a Catholic perspective (and a critique of the "new religions" ), in his letter "Spe Salve" (starting at Section 16, link at end):

My summary of the sections:
16. The discovery and development of the scientific method introduces a new era in human thought.
17. People used to hope in God for salvation; now, this hope has been replaced with "faith in progress".
18. It seems like reason and freedom, by themselves, will guarantee progress and lead to a better world. However, people often saw reason and freedom as being in conflict with the Church and the political structures of the time.
19. The French Revolution placed hope in reason and freedom alone leading to a better world. However, the second half of the French Revolution reveals that pure reason and freedom might actually lead to a worse world.
20. Marxism, and the social conditions leading to its rise, are discussed. Marxism does not hope in Science to provide progress, but rather hopes that Politics will provide progress, by calling for revolutionary change.
21. Marxism doesn't work either. "[Marx] forgot that freedom always remains also freedom for evil. He thought that once the economy had been put right, everything would automatically be put right." "...it is not possible to redeem [man] purely from the outside by creating a favourable economic environment."

[w2.vatican.va]

A scientific theory can only be regarded as fact when other scientists, independent of the first can duplicate the finding by experiment

The illuminated ones want to tell us it's settled while withholding the data they used from us.

They also condemn skeptics (those "Climate deniers" ), whereas real science invites sceptical inquiry

They want to change the rules when winning doesn't happen, like they want to eliminate the Electoral College because Trump won by a large margin

If Obama had won by half that margin the MSM would be crowing about "The Landslide"

Certain idiolougs will affirm 'science' if its backs their argument/agenda. But science facts , for example there being only 2 genders, is not acceptable and either the 'science' is still out on that or its just 'hate speech '. True scientists will work on provable facts and reproducible results but if their results contradict certain agendas they get shut down and possibly shunned by their peers. So i guess todays state of science is much like the political climate of the Catholic church at its height of power.

I believe it's relative to the topic. AGW has become a religion. Its followers believe without a doubt that it is happening and become furious when you question it. The CDC expects us to inject our children with every single vaccine it can come up with. When we ask whether its necessary or safe they throw the word science at us. In that case I would say science has been hijacked by the state. I am having trouble thinking of an example of a religion hijacking science.

None of the above. A legitimate scientist welcomes and learns from refutation. No science is ever "settled".

Regarding the free speech controversy, I support the statement: Anyone who says "I am in favour of free speech, but ... " is NOT in favour of free speech. I despair for the future of academia if this trend continues.