Definately LE. In fact likely one of the better examples* of LE.
And do not read The Sheppard's Tale unless you want Book totally ruined.
Oh man, really? He was my fav character...
Can you give me a spoiler of what they ruined?** spoiler omitted **
After reading that, I had to agree that Firefly dying might have been a good thing.
Wow. It's a good thing I didnt read that.
I always took the Operative's arc in Serenity to be Book's Arc. So while they never got to Book's actual backstory, I feel that they were showing you his arc through the Operative. It hit me after the first viewing, especially after Mal and the Operatives exchange on the landing platform as the Operative is leaving.
I felt the same thing. In fact I had a little pet theory that the Operative was really a clone of Book, that Book use to be an operative and that the reason Book left was because he was with the original group that discovered what had happened on Miranda.
As for the Operative's alignment? Definitely LE at the start and possibly LN at the end.