I'm not sure it matters what the author is thinking. The point remains that under an ethical doctrine that a great many people - perhaps most, I'm not sure - tend to espouse, one does have to concede that the Empire really isn't so bad.
I wouldn't go so far as to compare the Rebellion to ISIL for various reasons. But it's true that the Rebellion and the Old Republic had a strong theocratic undercurrent going on, and that's something to think about.
If anything, I think the article's compelling because it asks us to have the courage of our convictions. Regardless of whether you (or the author) side with the Rebellion or the Empire, a realistic analysis of the story is much more complex. And that's valuable, because the real world is complex, and yet it's very common for us to try to cast current events in terms of the simplistic moral narratives we learn in stories.