Sony confirmed the letter is legit and says that they also offered to meet with the Church to discuss their grievances. The Very Rev. Rogers Govender said they'll accept the offer to meet, but says they've still got issues. Yeah, like where's their money? The Church of England went into this for a payday. Originally the Church started off saying they were shocked that a "place of learning, prayer and heritage [was] being presented to the youth market as a location where guns can be fired," but in the end, it just comes down to money.
Sony's letter did make one point very clear. There is no connection between "contemporary issues in 21st century Manchester and the work of science fiction in which a fictitious 1950s Britain is under attack by aliens." We'll see what happens after Sony meets with the Church. Ethically, the final outcome should be announced publicly considering the Church made such a public stink in the first place.
Update: We did contact Sony to receive the full contents of the letter abridged by the AP. They informed us they are not making the letter public. Sony also said, "We believe that our letter adequately sets out our position and we look forward to showing the Cathedral authorities the game in its full context."
Update 2: The Sony letter as reprinted by the Church of England found after the break