I wasn't too thrilled about the ending either. It left so many questions unanswered, but then again, many of the Anime nowadays leave the endings with unanswered questions, so it is nothing new. I feel that religion in the series is loosely used as background for the story. Kind of like NGE uses religion loosely for its background info.

Chrno Crusade is a good series, just too many open issues in the end. Maybe they will make an OVA to answer some of these questions.

If anything, I feel the writers wanted to make the ending startling and unexpected, so not as much religion based.

Also, Rosette was a very scandalous person with her side slit dress, and there was a pervert inventor at the church. The writers appeared to want to write an entertaining story, not an accurately religious one.

In the series, I think the sinners were known as such because they went against the order of nature. Aion looked like he wanted to bring chaos to earth as he rebeled against Pandemonium.

If I were to interpret the ending, I would say that god only observes the people on earth, and does not directly get involved. He is either too busy elsewhere, or he probably wants to see how the people of Earth deal with problems. Aion is like Lucifer, trying to influence the world and events into evilness. In the end, all things will become chaos and be destroyed because human nature is inherently evil. That was why Rosette was easily influenced and influenced the masses against the Mandalan Order. Also, the masses are weak mentally and physically. The people were easily influenced by evil, and the only ones able to fight the sinners were the other Pandemonium and Chrno.

Anyway, I believe you should not take the story too religiously. It is there for entertainment, and should be left just that. I definitely have more faith in humanity than many of these writers (in other Anime as well; ie NGE, Gilgamesh, etc.), and believe that the future will be a peaceful place with advanced technology... A bright and happy place.