The game features the place of worship in one of its many levels - when the Church of England found out a month ago it threatened legal action, and the tabloid press had a field day with the story.
Today, SCEE has put a notice in the Manchester Evening News offering an "unreserved" apology that the game caused offense - adding it won't be featuring the location in any future games.
David Reeves, president of Sony Computer Entertainment Europe, said: "It is clear to us that the connection between the congregation and the cathedral is a deeply personal and spiritual one.
"As a result, it is also clear that we have offended some of the congregation by using the cathedral in our science fiction game.
"It was never our intention to offend anyone in the making of this game, and we would like to apologise unreservedly to them for causing that offence, and to all parts of the community who we might also have offended."
It is understood that no agreement has been made to change the current game or remove it from sale, but the dean of the cathedral said he fears it may happen again to other religious monuments.
The Very Reverend Govender told the BBC: "We still fear that the next buildings to be cloned for virtual desecration could be a mosque, synagogue, temple or other church."