The film was to be the first of three adapted from Philip Pullman's His Dark Materials trilogy but studio New Line reportedly watered down elements of the story under protests from religious groups.
Plans to adapt Pullman's follow-up books The Subtle Knife and The Amber Spyglass were shelved following the relative commercial disappointment of the first film.
Weitz told Metro: "They felt they couldn't deal with having a film that was going to cause religious controversy. But it would've been a different story if I'd had final cut."
Asked if he had any regrets about the situation, he replied: "It's the greatest professional regret that I have."
He compared directing to being Charles I of England, quipping: "Parliament can always cut your head off."
The Golden Compass was voted the most disappointing movie adaptation by Entertainment Weekly in 2008.
Weitz previously admitted to having a "bad experience" making the film and blamed the studio for "emasculating" the project when they "took the religion out of it and tried to turn it into a popcorn movie".
Author Pullman later cast doubt on the possibility of the sequels being made and suggested that opposition from the Catholic Church may have put people off seeing the film.
> American Reunion looking really good, says Chris Weitz
Watch Chris Weitz's recent interview with Digital Spy about making Twilight: New Moon below: