Although about 99 percent of the more than 50 million Turks are Muslim

Difficult to explain, but let me take a shot. This is pretty similar to the one of OG questions "In 1791 Robert Carter III, one of ...". Have a look into this link:
in-1791-robert-carter-iii-one-of-the-wealthiest-plantation-138325.html

Basic concept: the before a category is either referring to abstract class or complete/total members of that class.

From abstract perspective: "Use of coffee is bad" is wrong though "The use of coffee is bad" is correct.
From completeness perspective: "A Cat is good" mean that one particular cat is good though the "The Cat is good" mean that cat as a complete category in toto is good.

In B, construction of first sub-clause is like: About 99 % of over 50 million of the Turks are Muslims.
As per our completeness/totality perspective, placement of the before Turks will mean that author is referring to the complete/total worldwide population of Turks and not just the Turks in the republic.

Now let us take a closer look at A and C..
In A, construction of first sub-clause is like: About 99% of the X are Muslims.
In C, construction of first sub-clause is like: About 99% of X are Muslims.

The only difference between A and C is around the. The author want to consider the complete population here while giving his argument, so A makes more sense. If you don't place the, it will not consider that the noun here represent complete population.
If you still have problems in visualizing why C is wrong, have a look into C on this link. For first question(In 1791....), C is wrong and for second question, (As a result of the ground-breaking work), D is wrong. Both of them are wrong because of the very reason that absence of the makes the quantity of class non-complete or less than total.

over is considered good only with spatial references[The cup is over the table], so E and B are down.
The presence of 'Despite the fact that' made me frown on D and E. I would have preferred "Despite that" rather than "Despite the fact that" in a GMAT question. I am yet to see a GMAT question correct with this usage. I think it was the presence of word fact which made me worrisome with D and E as presence of fact is generally redundant in GMAT questions, unless word fact is explicitly needed to support the meaning of the sentence.