The actress and singer received the group's Vanguard Award, reports Variety.
The Glee guest star said that being "a Christian and also a gay-rights advocate is one of [her] purposes in this life", adding: "It's a very big dichotomy, but that is exactly what I believe."
Speaking about growing up in Broken Arrow, Oklahoma, Chenoweth recalled: "People had to hide who they were. I don't think God wants us to do that. But I realise that not everybody believes like me."
The 42-year-old, who recently joined the cast of ABC pilot Good Christian Bitches, added: "Christians, even if they disagree with a certain lifestyle, would be remiss not to look at what this is about: human rights. I don't judge them, but I don't want to be judged for what I believe."