We definitely have an independent clause on either side of the semicolon in choice (C):

1) "only 36 percent of the nation’s 607 HMO’s were profitable last year" - the verb is "were", and the subject of that verb is "36 percent" (36 percent of what? of the nation's 607 HMO's).
2) "it estimates..." - the verb is "estimates", and the subject of that verb is "it".

It doesn't matter that #2 wouldn't make much sense on its own. Take this pair of sentences, for example:

Tim is a friend of mine. He often loans money to me.

If we get rid of the first sentence, the second one doesn't make as much sense (who does "he" refer to?). But that certainly doesn't mean that the second one isn't a grammatical sentence. The same goes for option (C). The second independent clause might not make sense on its own, but it's a complete thought with a main subject and verb.

As for the pronoun "it": well, what singular nouns could "it" refer to? The subject "36 percent" has a plural verb ("were") and would therefore require a plural pronoun. The only singular options are "Interstudy" and "a nonprofit organization", and those two nouns refer to the exact same thing! We can replace "it" with either "Interstudy" or "a nonprofit organization" and get the same exact meaning.

I hope that helps!