I don't know if the dinosaurs are portrayed as *more* immoral than humans. They were arrogant, just like humans, and saw less developed cultures as inferior, just like humans.
I thought the episode was a little too silly. If they were going to introduce a race that was much more powerful than humans they shouldn't have completely ignored that this was an established part of the universe.
And yeah, the cities would have been long deteriorated after 65 million years. But they would have left behind a whole lot of metallic alloys.