This is rumour and conjecture, but I believe that BA Handling at MAN have not been very popular with the Manchester Airport Authority for years due to their reluctance to accept diversions, and their treatment of them once in (Diversions of widebodies = welcome cash for the Authority during the leaner winter months of course). Manchester on a winter afternoon is a relatively quiet place, and as you say, Terminal 2 could easily have handled them. Having said that although T3 isn't huge, it isn't snowed under (sorry - couldn't resist it) during the afternoon with just a gentle trickle of Embraers.
The BA spokeswoman in the Evening News article states that they only have 2 stands capable of taking 747s, and they were both occupied - by what is my first thought? The only widebodies on T3 nowadays are the AA and BA 767s, which were both long gone by the time QF31 arrived, so they must have been occupied by 146s or Embraers, which will have either been on a turnround, or not in use, and so moving something or making a gate change wouldn't have been a big deal at some point during the 5 hours that this was going on.
I could be wrong of course - one should never underestimate the Airport Authority's capacity for bizarre behaviour but on this occasion it smells of a local BA problem.
Edit to add the URL to the article online:
http://www.manchesteronline.co.uk/ne...ory=48800.html