Can Atheism become corrupt like religion?

[Jenny A]

I'm curious to find out if most atheists hate the 'ancient alien' theory because it goes against "evolution" dogma of Atheism.

Beginning at the beginning.  An atheist could certainly believe in the "ancient aliens" theory and still be an atheist.  An atheist could have no beliefs whatsoever about the origins of humans, or life, or the universe.  All atheism is, is a lack of belief in god.
My personal lack of belief does not hing on belief in evolution.  It hinges on lack of evidence of a god or gods.  There were atheists before the theory of evolution and there would still be atheists if it were disproven tomorrow.

According to Darwin's theory, it should have taken humans millions of years to evolve to the intelligent species that we are today.
Here's my issue: and why I think 21st century Atheism is no different than 14th century Catholicism dictatorship. In the 14th century if you said the earth might not be the centre of the universe "you'd be hanged on the stake". In the 21st century if you say the universe might of been created by intelligent design 'you're career is over and you'd be labelled as a quack".
Meanwhile, in the 14th century. Hidden from public attention a small group of mathmatecians and scientist were secretley trying to figure out how the universe worked and prayed that they didn't get caught trying to do something blasphemous like going against the 'status quo". Same thing in the 21st century "theist scientists and even agnostic scientists" must surely be secretley be in the closet trying to figure out "the status quo tells me 'Do not look there, there is nothing to see there", but I feel they are wrong".
Today, as a scientist. If you so dare go against the 'status quo' of Atheism you lose your job.

Buzzzzzt.  Wrong.  It's true a much higher percentage of scientists are atheists than the general public.  But there are many openly religious scientist out there.  In the U.S.:
 

[F]our-in-ten scientists (41%) say they do not believe in God or a higher power, while the poll of the public finds that only 4% of Americans share this view.

  Pew Research Center

Do you feel - Atheism is slowly going to become corrupt like religions? Scientists will not be permitted to look into 'supernatural' or 'mistisism' and try to find a scientific reasoning - as it would be deemed blasphemy and heretic as an Atheist society.

The scientific community and the atheist community are not a single set of people.  They are two overlapping sets.  And they are different categories of sets.  Atheism is by definition, just a lack of belief in a god or gods.  It isn't a system of belief or a method.  It may be informed by science, i.e. one could use the scientific method to determine that god is not a reasonable hypothesis.  But one could reach the same conclusion philosophically, or just by gut instinct.
Science isn't a belief or lack of belief, it is a system for determining the truth of factual claims and determining how the world works.  It depends upon explaining the evidence and making and testing those explanations. Various supernatural claims have been scientifically tested:  ESP, telekinesis, etc.   Some supernatural claims, are not testable because they have no predictive value--if the nothing in the real world will be different if a claim is true or not, that claim is not testable.  It has no scientific value.  I see no signs that the scientific community refuses to look at testable supernatural claims, only that: 1) there appears to be little if any replicable evidence supporting such claims; and 2) so far no good testable hypothesis for how such supernatural phenomenon work has been suggested.  
The world supernatural is a little odd from a scientific standpoint anyway.  If a supernatural claim were proven and demonstrated to have a cause, then it would no longer be supernatural.  Let me give you an example.  Suppose you showed a smart phone to an extremely primitive tribe that didn't know about electricity, let alone computers.  Your phone would appear supernatural.  But if you showed them how it worked (an explanation of years), then it would cease to appear supernatural and be what it obviously is to us, a part of the natural universe. It is for this reason that "it's supernatural" or "it's magic" is not a scientific explanation.  It's just another way of saying we don't know.
Scientists can believe in the supernatural, theistic, or any other unsupported claim.  What they can't do, is call that belief science.
I have a hard time imagining as diffuse and diverse a group as atheists becoming authoritarian, though a group of atheists might.  So far there doesn't appear to be a cabal of atheist scientist trying to control all scientific hypotheses.   The result would cease to be science if such a group gained control of it.  Science is by definition without bias as to the results of the method.