I wouldn't worry about that. Technically, the entire amount is income but then when figuring the SE tax, you get a partial deduction that accounts for the amount that a regular employee has paid on their behalf. So just reporting the income without the counter deduction will result in you overpaying.
I also don't know how the church could fix since, even if they filed amended form 941 or 944 to remove the withholding and got a refund from the social security administration, any money they refunded to you would be income in 2018 under the cash basis accounting rules.
For 2017 I would just stick with the W-2 as written and pay SE tax on the housing allowance only. Make sure the church fixes the issue in 2018 -- they may not have even filed the first quarterly form 941 yet and even if they did it's much less complicated to amend that and refund the 2018 withholding to date.
If you really want to try and have the church correct the 2017 filings, you will need the help of a CPA who deals with churches and you probably need to file an extension on your personal tax return while things get straightened out. I'm not sure it's worth it.
