Much of both the government and the general public dislike therianthropes. They are scared they will attack people, and to be fair, many theris have, especially theris who first transformed while being attack or cornered. The transformation is triggered by emotion, and many theris lose touch with their human mind during their first transformation. The Pack and some ferals have found ways to transform at will, and to keep their minds when they do.
One of the more subtle reasons for the shoot-to-kill policy came from the Centre for Disease Control: if therianthropes turned into animals, then it stood to reason that they could catch animal diseases, and if they still had them when they turned back, they could then spread the diseases to humans.
Sanctuary was established because running a prison for theris got expensive, and possibly also for other reasons. At the same time as the shoot-to-kill policy started, the DTC started doing something really manipulative. Instead of telling the theri’s family that they had transformed, whenever possible, the DTC told them their relative was killed in a theri attack. Sometimes this wasn’t possible, because too many people saw the person transforming, or too many people saw that the theri was a turtle, or something else that can’t inflict all that much damage. Their reasoning was that the fewer people with a personal connection to a theri, the fewer people there would be who cared how they were treated; and the more people who knew someone killed by theris, the more people there would be who would believe theris were dangerous.