"Is this like Microsoft asserting control over what programmers may code for Windows?"
Absolutely not! Windows is an operating system whose principal purpose, like all other operating systems, is to provide a platform on which applications can run without having to control hardware directly. Who writes the applications is largely irrelevant, just as it is not in the operating system writer's interest to restrict who can write those applications or under which terms (that's not say they can't do so, just that it's not in their best interest).
The simularity between WoW's "engine hooks" and and Windows' APIs is merely that -- a simularity. WoW is itself an application written with Windows' APIs. WoW /needs/ the operating system in order to run, just as WoW's players need Windows to be able to play the game (Mac version and Wine notwithstanding). Windows, however, does not /need/ WoW in order to exist (though it certainly doesn't hurt Microsoft's bottom line).
One can, of course, state the parallel with WoW addons -- that they /need/ WoW's "engine hooks" to function, but WoW does not need user addons to provide a playable game experience. The principal difference, however, is a commercial one...
Applications, not operating systems, are what sell PCs (and its hardly deniable that a large percentage of WoW players likely have PC's in the first place just to play WoW :-p ). Yet, the applications need the operating system (nevermind that an application /could/ be written to talk to the hardware directly), thus it is in Microsoft's interest to make their operating system APIs available "without restriction" to application writers -- in order for the operating system to sell, there must be applications written for it.
Contrast this to whether WoW needs third-party addons written for it for WoW to sell... it does not. If you, a WoW player, bought WoW (and pay monthly fees to Blizzard), simply for the sake being able to use, say, QuestHelper or Auctioneer then you, "sir" are... well, let's just say among a great minority of players from whom the addon writers are also justified in charging fees and claiming the right to do so...
Yet, were this case, then I'd argue that Blizzard would be equally justified in charging additional "license fees" to the addon writers as well. They do not, of course, since though addons might make the game more "enjoyable" for some players, without them Blizzard would probably still have the most successful MMO currently running.