Well, I think the chorus in "For the Greater Good of God" is meant to represent "human suffering" - that is what the song is all about anyway to me, to canalise that feeling, you know make a clear point about the message that is presented during the verses? Bruce sounding strained during the chorus is just a part of this effort - it's a theatrical production.
But this song is not for everyone! It's definitely challenging. But if you pay attention to the message that is presented - I think you can grow to accept it.
Without the repetition it would not have the same effect. Harris' best epic. It's somewhat funny there's such a difference between the Bruce penned lyrics to which you need an encyclopedia to decipher some allusions at times. There's beauty in Steve Harris writing clearly and hammering the point home. It doesn't make it simple, or bad.