I don't know what state you live in and there may be an issue on a state level of making a yearly payout, but I don't see any issues on a federal level for doing that.
Even though many states require that employees be paid on at least a twice a month schedule, it is a housing allowance and not salary, so I don't think that would be an issue. AND the minister's exemption usually exempts them from some of those dept of labor regs.
So...unless someone can chime in with something different...I don't see an issue with paying the housing allowance out yearly.