If we take prophecies into account, it would make perfect sense for Kara to be the one piloting Galactica into the colony. She is after all being called the bringer of death and we could consider that Galacticas is the dying leader as it is the flagship.
The word used is "harbinger" which the N.O.D.E. defines as "a person or thing that announces or signals the approach of another", so she's a herald, in effect. Since they do not know where the colony has gone to, and Anders now appears to be a hybrid, it actually makes much more sense to allow him to find it otherwise his whole transformation is pointless, as are the comments that only the firewalls are stopping him from taking over the computer systems and that he may be able to take control of the FTL drives.