If this doctor says long term use of Iodine leads to Hashimotos he is not an Iodine literate ptactitioner because he doesn't know the protocol. He hasn't read Abraham, Brownstein or Flechas completely or read about the people who got rid of Hashis on Iodine with a specific technique.
Does he have you taking salt water every day and using selenium? And taking the other companion nutrients?
Hair loss is associated with low thyroid and bromide exposure. The hip pain sure sounds like Lyme. Many of the Lyme docs recommend iodine because it is a spirochete bug that responds to iodine. It also helps kill the Lyme co-infections and candida.