According to the Lord's Prayer, God's will is done in heaven. This is Matthew 6:10:
On the other hand, Revelation 12:7-8 describes John's vision of a war in heaven:
I don't see this as a true problem. Presumably, God's will is done in heaven the vast majority of the time. We can give Jesus a little poetic license here. "Your will be done, on earth as it usually is in heaven" doesn't have quite the same ring to it.
Anyway, even in the example from Revelation, we can say that God's will is indeed done, since the enemy is defeated.