Emma Jeffrey says she was dismissed from 1st Abbeydale Rainbows last week after breaking a rule that youngsters recite a secular pledge introduced five years ago.
The 45-year-old, who had been volunteering at the division for seven years, was quoted by the Daily Mail as saying: "I'm not trying to shove religion down people's throats - just offering them a choice.
"The very name Rainbows is taken from the story of Noah's Ark. It was a given to Noah as a gift from God."
The Rainbows pledge was reworded in 2013 with the phrase "I promise that I will do my best - to love my God" changed to "- to develop my beliefs".
Girlguiding told Premier it is open to girls of all faiths and none, and each of its 100,000 volunteers are expected to adhere to a code of conduct.
You #InspireGirls as a Girlguiding volunteer no matter your age. Ellie saved her local Rainbow unit when she was just 18... https://t.co/i5qXFJisXi pic.twitter.com/ntVYEmYgRc
— Girlguiding (@Girlguiding) November 22, 2018
The spokesperson said: "We have one version of the Promise which is used by all members of Girlguiding.
"The wording of the Promise was chosen after a large consultation with our membership, who stated that they wanted to be united by one Promise rather than differing versions.
"Our members promise to be true to themselves and develop their beliefs. It is up to the individual girl taking the Promise how they interpret that."
Emma Jeffrey said she continued using the old pledge and that she was warned by the local County Commissioner Karen McFarlane that this breached organisational rules.
After being given an ultimatum - to omit God from the pledge or leave the organisation - Emma said she continued to give families the option of using the Christian pledge.
Emma was subsequently informed that she had resigned - something she contests.
The Girlguiding spokesperson added: "We're aware that a Girlguiding leader recently resigned from her role following a complaint made that she wasn't using the standard wording of the Promise.
"The leader was not withdrawn from Girlguiding.
"The complaint is currently being handled internally in an ongoing process so it would be inappropriate to comment further at this time."
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