Just finished the story. By far one of the absolute best stories I have ever read. If it was available to buy in hard copy, I would buy is in a heartbeat. Couldn't get into the whole lesbian thing, but it was only a teeny-tiny part of the book, not even that important to the story overall, so I can ignore it. The writer is really good at building suspense, and knows how to use climax correctly. A real page turner, I finished it in a week it was so good. I love the characters, and a couple places broke my heart. I guess if you wanted to know all that I was feeling, you can look at all the different emotes available on the site, and that still isn't enough.
Truly deserves the LEGENDARY tag on Equestria Daily.
EDIT: I was waiting till I finished the story before looking at the one year anniversary post on EQD, and since I finished it, I went and took a look. Apparently there are some ponies that are planning on getting it printed. Gotta start saving money.
As for protection of woman, I see it as a an urge that is genetically engrained into any good man/stallion. It's only natural that we would get riled up when someone we wish to protect is hurt.