Had the decision been made by municipal officials clearly based on anti-religious sentiment, then it would be a violation of the Charter. But that's not what happened in this case. The decision was put to a popular vote, and in those circumstances citizens are free to choose their response on whatever basis they wish.

One hopes that when Canadians vote that they avoid discrimination based on "race, national or ethnic origin, colour, religion, sex, age or mental or physical disability." However, Canadians are free to vote based on those criteria or any other.