I would say don't even think about this kind of stuff. The GMAC is removing questions that have a geographic bias and this is most definitely one that falls into this category as native speakers are much more likely to have seen this phrase.

Otherwise, stick with the most concise way to deliver the message - it is not really a coincidence that C is the shortest.

Not convinced with C.
C used had known and then discovered.
Discovery must have happened before the act of the scientist's knowing it happened.
Hence using past perfect tense for known would be wrong.
In fact, all uses of had known should be wrong.
Correct answer should be between A and D.
I chose D as it seemed better worded.

Moreover in C the usage of Past perfect tense looks wierd...

the below mentioned is an esoteric xplanation,.,.

personally i have observed that
to make sure word 'that' is used properly, the sentence before the word 'that' should answer the question 'what'. If it does , then usage is proper. u jst observe in few sentences. (smtimes it helps between 'that' and 'which' )

for the above question, i doubted C as the answer but my eyes were checking for the spoiler!!

C) For a long time, the scientist had known with great certainty

D) For a long time, the scientist knew beyond a shadow of a doubt

C answers our question
if we ask 'what' question C answers rightly

C-For a long time, the scientist had known with great certainty WHAT?? that.......

D) For a long time, the scientist knew beyond a shadow of a doubt (does not answer)
For a long time , the scientist knew WHAT?? beyond a shadow of a doubt, here if THAT was used after knew then it was fine.......

hope atleast it helps in this one..(if we doubt official answers we are utilising 0% of our time)
read smwhere!!
hope it helps..