I'm not convinced a cinema screening is the right place for an "advert" for a religious group. It's not really an advert in the true sense of the word in any case, we're not talking about Coca Cola here, or the new Ford Focus, we're talking about religion, and specifically the Church of England. I'd say this was more closely linked to a party political broadcast than it would be to an advert for beer or perfume. People aren't going to get riled up, offended, or agitated by an ad for the new iPhone 6, there's the definite possibility that some would be by religious content, whether that be because they are anti religion as a whole, or simply don't associate themselves with the specific religion in question. I don't believe you can judge the two types of "advert" equally, they are very different things.
For me an advert promoting a certain religion has no place in a movie theatre, in the same way that a party political broadcast has no place there either. I'm also not convinced that showing this advert in cinemas would actually be worthwhile in any case, I struggle to see the scenario whereby someone sits down to watch the latest blockbuster, sees an advert about the church, praying etc and thinks "I must drop down my local church on Sunday".