I've been wondering about this.
I went up to the Cathedral for a look around when they were filming so was keeping a close eye on the scenes I expected to have been shot there.
Now I could be wrong, but I'm not 100% convinced that the Cathedral shot scenes actually ended up in this film, (being saved for part 2 perhaps, or just cut?).
Like I say I could be wrong, but when I had a look around there were some very noticeable large Norse statues placed around the cathedral none of which I can remember seeing in the finished film. The other thing is that why would they bother filming in the Cathedral if the whole thing was just going to be shot with CGI backgrounds, they would surely have just used a studio rather than a location shoot?
That said, they did thank "Durham Cathedral in the end credits, and if that scene in the film is the one they filmed there then like you say, you'd never be able to tell.