It seems to me that Form 5329 would only have been created with code 12 on line 2 if you explicitly made an entry of an amount for Other reason exception for a distribution mistakenly entered with code 1 that you subsequently corrected. Make sure that you actually did select code W on TurboTax's 1099-R form. You should be able to simply delete the Form 5329 and it should stay gone.
