it's not about the story and lore, it's about the characters and psychology! You're missing the point!

You don't have to be a hero or to be selfless to have any connection to a cross. And Gendo isn't really selfless because he is doing it for his wife.
There are Japaneses christians but even if it weren't, a big part of chritianity is to spread the gospel so cultural appropriation doesn't make sense in this context because that is what christians want to happen.