Responses
I do think Mc is too nice but if you think about it, he came from a modern world and was a nice japanese doctor(they are usually very polite and committed to their jobs like mc) so his attitude can be somehow acceptable. Now I don't think the are not gray characters here for instance the apostles and the Pope are a good example. It's just that mc is being protected in the world tree so he haven't had the opportunity to face too malicious people. Let's remember he almost die 4 or 5 chapters ago xD
As a MC I feel annoyed by his too saintly character but as a doctor it is exactly just right. The story lacks morally gray supporting character to help MC deal with threats since MC is too nice. The story probably will surround MC turning enemies into allies or use luck to deal with enemies.