I disagree with the comment about this being 'bad English'. In fact, this is an example of correct, standard English. The 'it' is an impersonal 'it', sometimes called a 'dummy subject'. Here are some other examples with 'worth': Is it worth getting a taxi? It's worth having a look at this book. I don't think it would be worth going home now. As you can see, there's nothing wrong with this sentence at all.

You have three occurrences of "it" in that last sentence, and each one of them functions in a different way and refers to different things: 1. "It was pretty dark and nasty ...". This one is an impersonal usage, and the "it" doesn't refer to anything. Another name I have heard for it is the "weather it", because it is used in expressions like "it is raining". 2. "It was totally worth ...". As Su.Ki. explained, this is a dummy subject. It refers to "to avoid Fregley", and indeed, you could rewrite this with that as a proper subject: "to avoid Fregley was totally worth crawling ...". But the dummy subject construction is more natural, particularly if the infinitive phrase becomes extended. 3. "...crawling through it...". This one is your standard personal pronoun, referring to the drainage pipe.

'It' refers to the action described above, of crawling through the drainage pipe. Maybe there's some confusion because the word is repeated 3 times in the last sentence, and in two of those cases is substituting for the same action. In fact, this is bad English, which the author is probably using for effect. To make it clearer, imagine the following conversation: A: 'Was it worth it?' B: 'Was what worth it?' A: 'Crawling through the drainage pipe to avoid Fregley?'