If she had not converted, Peter would have been excluded at the time from the line of succession. As I said before, he would have been reinstated, however, in 2015 when the Succession of the Crown Act 2013 came into force.
Obviously, when he got married, Peter could not have foreseen that the law of succession would be eventually changed in the future to remove the ban on marriages to Catholics and that the change would be retroactive. I don't know the details of his engagement to Autumn, but I suspect she was told she had to convert for the engagement to go through.
Prince Michael of Kent, who was much further down in the line of succession, married a Catholic and accepted the sanction of losing his succession rights at the time. He is now back as 45th in line.