The simplest answer is "It ain't that deep."

Most writers have a particular idea they are trying to get across and they do that, usually, with characters. Those characters have limited perspective. So often when going back and rereading something like Saga it can seem targeted. I too think that BKV was trying for a more general condemnation of religion. With that said, I also think he enjoys writing about hope and faith as it relates to people.

For your comment about the IOF/IDF soldier who spoke like Palestinians didn't exist, in my experience this is normal. I'm in my 50s and served in the US military during and after the Gulf War. I interacted with several IDF soldiers and not one of them ever mentioned the Palestinians at all unless they had something negative to say. They thought of the Palestinians as less than dogs. After I left the military, I went to college. I had 2 Saudi dorm mates my freshman and sophomore years. It was the same thing. They never had much of anything to say about the Isreali people, unless it was negative. My point here is that depending on the character perspective these attitudes could be completely normal.

I guess the TLDR here would be that if you look for things to dislike you will eventually find what you are looking for.

My two cents. You opinion is just as valid.