The Rev. Boon Lin Ngeo, a Malaysian Protestant pastor whose message of tolerance for homosexuals has drawn fire in his country, sat with his male partner on a lime-green sofa inside the Office of the City Clerk in New York on a late summer day, where they waited their turn to be married.

The banality of the scene — the plastic-sealed bouquets, the bureaucratic march of couples through the office — masked the roiling effect that Mr. Ngeo’s nuptials have had in Malaysia, where Muslims are a majority and sodomy, even among consenting adults, remains a crime punishable by as many as 20 years in prison.

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