Distributing it via Windows Update does give Microsoft an advantage, and I have no idea if a judge would consider it anti-competitive. Every anti-malware app has its own facility for downloading updates and virus signatures automatically; it's a little precious to insist Microsoft use something other than its best-tuned update service to do that when competitors have to launch new processes and take up new system resources to do it for themselves. That makes for an additional process for them, but more importantly, it's an additional hit on CPU cycles and performance that the customer doesn't need to take.
Let Microsoft download MSSE updates any way it wants. I'm annoyed that I have to look under the Optional Updates to pick up new virus signatures, rather than getting them automatically with the rest of the critical updates. Usually the Optionals are things like a newer version of Silverlight than the one I deleted the last time I accidentally installed it and saw a performance hit.
I'm happy to stick with that. Things Microsoft offers Optionally I can skip; virus updates, even if they're for an app that annoys competitors by being both free and competent, should be as automatic and troublefree as Microsoft can make them.