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There's nothing in the Constitution that says the government isn't supposed to recognize a world leader, regardless of his religion, either. The analogy was that people disagree with the flag being flown at half-mast for the Pope because they don't like the Pope, or his party. Just like people would disagree with the flag being flown at half-mast for a president because they didn't like the president, or his party. Or, possibly, even that certain president's religion.
There are clauses in the Constitution and domestic policies against the government endorsing religion - there's nothing about political parties. The analogy between the two is absurd.