The Time Lock wasn't undone; The Moment was powerful enough to get around it (as Matt Smith noted explicitly). Also, the event happened on the last day of the Time War, but the events in "The End of Time" were midway through the war (months or even years before). Presumably, the people the Doctor kicked back into the time lock had time to humbly reassess their selfish and destructive plans. Hell, the Doctor's mother might have helped engineer an overthrow of the Council in the interim, or the generals might have just declared martial law à la Egypt.

The Valeyard concept really needs to be addressed somehow, though.