I'm sure the good doctor doesn't want anybody urinating in his Tardis, so it will remain as a Police box, as people don't mess with a police box.
I doubt Jesus has ever met the doctor. Or the Master, for that matter. Last time I heard, he was calling himself the Father and the Son in the Holy Spirit (Christians say and
the holy spirit, but that's almost certainly a typo).
Besdies, the portapotty TARDIS always appears to be occupied. I think even the Catholics realize this. The priests' confession booth is probably in honor of the Lord's daring escape.