My question is: isn't Captain James Cook the object of the sentence, so shouldn't it be whom, NOT who?

Sorry, just saw that you already caught the since.
Another thing to note is naming, unless absolutely necessary, try to avoid progressive tense on the GMAT sentence correction questions.
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Hey All,

FOR REFERENCE:
C) Naming them supposedly since their
D) who so named them supposedly because their

Just thought I'd weigh in on this, since I haven't seen a correct explanation. First, two introductory things:

1) As far as I know, "since" can sometimes be used as a synonym for because, though not when it's being used in a way where it can be misconstrued (interpreted as EITHER time or cause).

2) While -ing words are not always the best construction, it is not useful to be crossing off answer choices merely because you see -ing words. They are common enough that it's not worth your time to separate them in your mind.

Okay. Now, let's talk about other issues here:

1) C is wrong because it lacks the "so named", not because of the-ing form. C makes it sound that he named them ANYTHING because of the wet rocks. But the idea is that he named them IN A PARTICULAR WAY because of the wet rocks. In other words, C could be used in a sentence like "The rabbits were dubbed Adam and Eve by the veterinarian, naming them because she was the one who found them". But we want to make a point that they were named THE GLASS HOUSE MOUNTAINS because of the wet rocks, so we need the "so named" part.

2) Who/whom. It is dependent on how the pronoun is used in the sentence, not what came before. I can say, "It was given to be by James Cook, who eventually ate it." This answers the question, "Who ate it?" "He did!" So it's a subject pronoun (though it was an indirect object, within the prepositional phrase, in the previous clause). In contrast, If someone asked me who gave me the cookie, I could answer: "Dave, whom I will see tomorrow." Even though Dave is the subject of the understood sentence "Dave gave it to me", he has now become the object of the main clause: "I will see HIM tomorrow".

Word.

Hope that helps!
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I couldnt get why since is wrong here. For C, OG says: the preposition since loses the important causal logic of the sentence.
But, since looks fine from synonymous and ambiguous meaning of because here. Am I missing something here?
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C is wrong because

comma+naming (comma+doing)
modifies the previouse clause and associate with subject "mountains"

this make no sense

Dear Manhantan expert

comma+namming

modifies the previous clause and associates with the subject of that clause

C means
mountains names them

this is not logic.

is my thinking correct?