Not at the church. Remember: Rin never saw her until this story and Tokiomi knows what Archer looked like.
He's paid by the Church. It's an actual job, you know.
It's how he managed to get all that expensive wine for Gilgamesh to steal in Fate/Zero.
Tokiomi is still in charge of that until Rin is old enough for her name to be placed on official documents.