Each circle is treated differently. For example the Rivaini cirlce was basically a school, and people were free to come and go.
It is important to note that the Chantry is not all powerful, and any nation's army would be more powerful than the Templar's in their nation. Different nations have different customs, the Rivaini revere their Seers, thus mages are granted special treatment there. Kirkwall, on the other hand, had a small military force and a large Templar garrison, plus it had a weak ruler who bowed to the Templar's whims, allowing the Templars to be stricter there than elsewhere.
Think of the Chantry like a 14th or 15th century catholic church, very powerful politically, fairly weak militarily (as evidenced by the numerous failed attempts by Italian Pope's to conquer various regions of Italy). The ability for the Pope to directly influence a nation was limited. In England the King officially broke from the church with some upheavel, but his nation survived the transition. France was fairly catholic, but even they often sided against the pope when his will conflicted with French interests (the Hundred Years War is a notable example).
Circles exist in sovereign nations, and as such are subject to those nations laws and customs.