So the ruling to question 1) is not clear. As its an item in your spell inventory that does not need refill I would allow to keep an uninvoked prayer. But as a player I would be interessted at a free Theologian skill.
You are right that 2) might be a possible solution. But after your GM gives you a wrong mayority you could perform a atonement ritual. You should be able to succeed an Ob 1 Ritualist test.
As atonement is a Test, it cost 1 check or is 1 cost in town.
As a GM I would also use a missed prayer for maybe helping the cleric by showing him how useful some of his unused prayers are… If I want to give a penalty a condition might be better.