***Spoilers Alert!*** One other big thing in Ender's Game was that Ender unknowingly wiped out the entire alien species, except for what looked like a worker and a queen. This reminded me of that story in the Bible where the Israelites where commanded to put the ban on an entire people, or tribe.
The Israelite king tried to save one person from this enemy nation, but the Israelite prophet Saul chastised him and killed the last one himself.
Just like the whole creation/evolution debate, this genocide problem in the Bible had been thought about from the beginning of Christianity.
The one obvious move was to deny that the Old Testament is really inspired by God or reveals a God that Jesus was talking about in the New Testament. This banning of the Old Testament was declared a heresy called Marcionism by the early Church.
Another option was to see if these and other vexing stories in the Bible (like the creation story in Genesis) could be seen as more allegorical. Origin of Alexandria was a leading proponent of this idea.
Father Barron can say more about this option.
I think this allegorical option is a good one, especially since the Old Testament, "contain[s] matters imperfect and provisional".
Ender knew that the genocide he unknowingly carried out was wrong. He tried to make amends at the end of the movie.
The Church officially has the same take on genocide, it is to be rejected. She is with Ender. She teaches that "One is morally bound to resist orders that command genocide."
Here's Part I.