The Maker created the blight, so I'm sure he isn't Tainted.
Alduin is like any other Daedric Prince in the aspect that his body is basically an avatar of who he is. Just like Akatosh, has his avatar of a flaming dragon, or Sheogorath has his avatar as a jolly old man in a suit, Alduin has his. That being said, Alduin is a being that is above the physical world of the humans where the Archdemon is. That's why we see his soul taken out of Mundus upon being defeated, because just like any Daedric Prince, when defeated they are only banished. Not killed.
Think of any other Daedric Prince fighting the Archdemon. Should the Archdemon win, the Daedric Prince will just return to their realm of existence, but they aren't dead. We look at who defeated Alduin, the Dragonborn. The Dragonborn had to use a shout to make him temporarily mortal in order to defeat him, meaning that he couldn't have been defeated in any other way.
The Taint, as far as we know, only affects you if the blood gets in your mouth or eyes (otherwise all your companions are dead). Alduin does not have to touch the Archdemon to kill it, and he's smart enough to use his shouts to his advantage. Also consider that Alduin is no stranger to fighting dragons.