More specifically did he know about it when he saw Jack in the alien bar? Please avoid spoilers from after end of time.
It's unlikely the Doctor knows for a number of reasons both meta, and in universe.
Meta: the late Torchwood's were tonally so different from the main show, being couched at at a level including things unsuitable for a general family audience [I do not mean LGBT issues] that to reference them in Doctor Who would be difficult. If the character of the Doctor is unlikely to ever be written as explicitly acknowledging the events of Children of Earth etc, then it is simpler to believe him/her unaware of them.
In universe: everyone concerned with the events is likely to be so ashamed as to not wish to parade their various levels of guilt before the Doctor.
Further, avoiding spoilers as much as possible, there is a degree of negative evidence later insofar as the Twelfth Doctor associates his new face with one point of origin and not another.