It's a fine song, but I wouldn't make too much of Dylan's theological interests and knowledge, which were probably quite superficial (at that time, anyway). When writing the song, he evidently thought that St Augustine had been martyred, which is not correct. He probably did't know anything specific about St Augustine, and just used him as a convenient symbolic figure for a 'prophet of doom'.
It's a fine song, but I wouldn't make too much of Dylan's theological interests and knowledge, which were probably quite superficial (at that time, anyway). When writing the song, he evidently thought that St Augustine had been martyred, which is not correct. He probably did't know anything specific about St Augustine, and just used him as a convenient symbolic figure for a 'prophet of doom'.