True enough. However, it's unknown whether or not Joss had already come up with Book's backstory before the movie. It's definate that he was involved with the Alliance, but the rank "Operative" wasn't revealed until the movie. It could be possible that Joss thought up that rank specifically for the movie and may not have anything to do with Book's past, just that he knows of them.
HOWEVER... In the novelization, the Operative is actually at Haven (SPOILER)when it was taken out. He specifically was the one who shot Book. It's of interest to note, that while admitting to have never met him, the Operative clearly knows of him regards him as a bit of an idol. (SPOILER)However he shoots Book, because Book shot down the Alliance ship. The Operative considered it inhonorable for a man of faith to murder "innocents", regardless of who Book used to be. The Operative uses his sword to offer honorable deaths, which he doesn't feel Book deserves, thus Book gets killed by a gun.
Based on this, it is quite possible that Book was an Operative or possibly of even higher rank.