If you have a look at the new DWM Moffat explains that the GI can travel through time. So he did think about it but quite rightly felt no need to mention it in the episode for the six people who'd get worked up about it.
Well, my general loathing of Tom Spilsbury has caused a DWM allergy but it's pretty cool he set the record straight after realising the error. I suppose maybe also, the Great Intelligence could view time in a non-linear fashion ala the Prophets in DS9.
The Badger wrote:
As I understand it, the Doctor's old friend Padmasambhava supposedly contacted the Great Intelligence on 'the astral plane'. Perhaps such contact transcends the boundaries of time and space?
This had occurred to me too and is my personal theory to reconcile the contradiction.