IMO, it's entirely possible that they consciously let away some apostates that "do good" outside the Circle like Hawke. Maybe the templars simply hadn't enough manpower to actually raze all apostates, so they simply choose to turn a blind eyes to "useful" ones.
This would also fit with Meredith's comment in Act 3 to a Mage Hawke if you get snippy with her, that both Hawke and their apostate friends only remain free at her descretion. As long as Hawke is useful and continues to do work for the Templars and serve the people of Kirkwall, they'll be allowed to retain their noble status, house and fortune and more importantly, their freedom.
It's not like Hawke can simply leave Kirkwall anyway in Act 3, since they're a very high profile individual, the Templars would immediately hunt them down and all of Hawke's forture and various assets are tied up in the city? Legacy and MotA also probably required a Mage Hawke to give the Templars some notice of where they were going and when they'd likely be back?