I believe this would be okay, with the following comments:

1. That the 1099-R reflects that the taxable amount is not determinable
2. In order to qualify, the housing allowance amount must be designated in advance.  I would recommend obtaining something in writing from the Church which shows that the housing allowance was in fact determined in advance.  
3. The housing allowance for retired ministers is no different than that or active ministers in that it is not taxable as long as it does not exceed the lesser of actual housing expenses or the annual fair rental value of the home (furnished, plus utilities).