First, if only one choice has a given meaning, it's probably not right unless the other meanings are clearly flawed. Second, it's hard to imagine that the rival would agree to a deal with the specific purpose of making this company the largest player. While that might be a clear consequence, surely that is not the *purpose* of the deal from their end.
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A few thoughts on this:

• Pronoun ambiguity isn't an absolute rule on the GMAT. More on that in this video.
• The "it" isn't underlined -- so there's nothing you can do about it! There's no reason to worry about an issue that won't help you to distinguish among the five options.
• Pronoun ambiguity is only wrong if it creates confusion in terms of the meaning (and if, of course, you have some clearer options available). And there doesn't seem to be much reason to worry about confused meanings here. The pronoun "it" appears twice in the sentence, and in both cases, "it" refers to "the computer company" -- so it's hard to argue that the second "it" causes much confusion. And the combined company would be singular after the acquisition anyway, right?

I hope that helps!
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The computer company has announced that it will purchase the color-printing division of a rival company for $950 million, which is part of a deal that will make it the largest manufacturer in the office color-printing market.

Let us zoom in on B and E


(B) million, a part of a deal that makes

Isn???t ???a part of a deal that makes??? a noun+noun modifier that can modify the full preceding clause ???it will purchase the color-printing division of a rival company for $950 million????

This makes sense because ???the purchase of the coloring printing division????????? explains what the ???a part of a deal??????..???
Also, how is ???makes??? incorrect? *a part of a deal that makes* could be giving a fact that now makes it the largest manu in the office color-printing division.


(E) million as part of a deal that will make???

How do we know that the author wanted to say ??? 950 million as a part????

The author could be wanting to describe the whole preceding clause. This is ???a part of a deal???

permit me to post another time.
look at choice C and E.
choice E means, the purchase is as a part of a deal. "as a part of a deal " modifies "purchase". this is logic
choice C means:
noun+noun modifier can modify the whole preceding clause. noun+noun modifier is the representation of the whole preceding clause.
so, choice C means
"it will purchase" and this phenomenon is a part of the deal
this is wrong. the event that "it will purchase" is not part of the deal, but only "purchasing" is a part of a deal.
the event that company A will buy company B can not be a part of a deal. only the buying can be as a part of a deal.

an event can not be a part of a deal. an action,verb can be as a part of a deal.

the company A control or want to do the deal and it take an action to finish part of the deal

honiestly, I want to explain why choice C is wrong this way. I wish you explain more why "a part of a deal " can not modify the preceding clause.