Of course, as an atheist myself I'll tell you why.
Getting married isn't a religious event, only if you get married inside of a church, chapel, or any other religious place.
As an atheist, I believe everyone has the right to get married, including gay and lesbian people.
Getting married on a beach say, would not be getting married in the Church, making it an unreligious event. It is not approved by them beforehand, and it is not IN the Church, so they do not write it in their records so they act is if you weren't married.
You may be confused, Matrimony is a religious sacrament in the Church. Marriage is something anyone can do, atheists and gays included.