Ark is 218 (262,144) light years away from the center of the Milky Way. As the Milky Way is around 100,000-120,000 light years in diameter, the installation is beyond the reaches of galactic space, thereby keeping anyone who is on it safe from the firing of the Halos.
Many Forerunners were on Ark during that time, that's why they survived.
[Edited on 08.17.2012 12:11 PM PDT]