That is Canadian policy if you have been arrested and there are charges against you or have been convicted of a crime you must apply for a special acceptance to come to Canada.
The border guards only have the info about the arrest that they get from the country of origin. If it doesn't state the charges were completely dropped then anyone would be denied entry regardless of if they burned a holy text or not.
My guess is if he had of done his homework to check on his own eligibilty for entrance into Canada they would have warned him about the potential for his prior arrest to hold him at the border. They would probably have also advised to carry with him the documentation to show that the charges for the arrest were dropped. If he had of done that I bet he would have been allowed into Canada within 5 - 10 minutes.
This is not a matter of "freedom of speech" rather the fact that Canada does not want other country's criminals coming here.
I enjoyed reading this post. +1