
Originally Posted by
GoktimusPrime
The Doctor wasn't only trying to thwart the Daleks, but the Time Lords too. At the end of the Time War, Lord President Rassilon wanted to invoke the Ultimate Sanction which would destroy all of creation, but the Time Lords themselves would survive as beings of pure consciousness. In principle the Time Lords were trying to do the same thing that the Daleks were doing -- to eradicate the universe of anything that wasn't their own race. The Doctor could not allow this, thus he was willing to use the Moment to destroy his own people rather than allow them to commit super-genocide across all creation (that would arguably make the Daleks' attempt at genocide pale by comparison). (re: The End of Time)
By shunting Gallifrey into a pocket universe, he not only protected Gallifrey from being destroyed by the Daleks, but also protected the universe from the Time Lords (principally Rassilon and his cohorts).