Are you sure about that? After all, the Bible itself is filled with people fighting, with God telling people to fight, and there is plenty of biblical imagery of God as a warrior. So, any notion that God is a pacifists can't pass the test of what God says about himself in the Bible.
Now, there is violence that the Bible does condemn, such as those who attack the innocent to rob them or even to kill them. Proverbs has much to say against such people, those who lie in wait to harm others, those who are swift to shed innocent blood.
But there is also Joshua, who led Israel to conquer the land God had given to them; Gideon, who led men to drive off those who were robbing them; David, who fought in many battles without God condemn him for such things.
So, no, I don't think I need to feel any guilt over watching an anime series that has fighting in it.