The first problem is purely classificatory -- it doesn't make sense to decide, sight unseen, that certain games are full releases and some are addons. Danger lies that way -- in deleting reason from your system of organization, you end up with a bunch of tinpot dictators and Brazilians insisting that whatever unreasonable thing they've decided must be right regardless of evidence. That's not how you organize anything.
What's more, though, there's no reason for it. Why should WCSO be an addon? As more intelligent people than I have pointed out in this thread, it doesn't add on to anything... but beyond that, Origin doesn't call it one. Secret Missions, Crusade, Special Ops 1 & 2, Tactical Operations, Righteous Fire, Forge of Virtue, Silver Seed, Lost Vale and so on are all expansion packs not only because they expand on a larger game, but also because that's what they're sold as. Secret Ops *wasn't* developed or sold that way - it doesn't make sense to insist that in your private little universe it secretly is. (Think of the Ultimas I just listed -- why is Serpent Isle a new game but Forge of Virtue not? There's your answer.)
The biggest problem is that people insist on the label in order to demean the game. It isn't worthwhile, it's just "an addon". That's a load -- Secret Ops was a very, very important release. It was a pioneering game for a genre that is *only now* being appreciated. WCSO invented the episodic game... years and years before SiN and Half Life and before companies could make ten million dollars selling extra Halo maps. Not only that, but it actually *does* continue the story in exactly the same way as Wing Commander 2 or Wing Commander 3 did. Secret Ops deserves our respect, not our petty idiocy.