I can certainly understand why someone who acknowledges no supernatural divinity would give his highest loyalty to his country.
Should a Jew give his highest loyalty to his faith over his country?
Should a Hindu?
Should a Muslim?
You wrote:
“I can certainly understand why someone who acknowledges no supernatural divinity would give his highest loyalty to his country.”
That’s not logically sound. How many athiests would side with their country if their country told them they had to worship God, go to Church, pay taxes to support the established faith, and not use birth control?
In the end, if that were the situation, an athiest must choose his conscience over his nation. If he doesn’t, he will hate himself, hate his nation, and be useless to society in any matter concerning truth.