Being difficult here, because it makes me uneasy, too, but... why? Do you also object to the national flag in the Sanctuary? Again, that makes me queasy, but there are enough UCA churches (let alone Anglican ones) where that's totally normal that I feel the need to ask the question.

Would the reason why it was there (as a reminder to pray for the President-elect in this week when he will be sworn in, for example) change your position? The standard format of the Anglican intercession prayers include the Queen and her family as well as political leaders by name. (Again, I don't so much like that, but Anglicans are v. establishment. Can't be helped, I suppose.)