My prefered choice is having Bethany and letting her go the circle. This does several things:
1. A big FU to Malcolm, you are a noble like you should have been, and bethany is in the circle like she should have
2. It makes hawke care about what happens to the mages, not about mages in general, but specifically about the mages inside the circle of kirkwall. There is plenty of room for good roleplaying there that is otherwise lacking. Your hawke can sympathise with the mages and want to free her sister, or think the circle is fine. If bethany dies or becomes a warden, then there is a huge disconnection when hawke has no reason to care about happens inside the circle: neither anders nor merrill are in there.
3. There is a dreadful short list of decent mages in kirkwall. We have many templars, ranging from hardliners to liberals: Alrik-Karras-Meredith-Cullen-Thrask
The mages are like: Grace-Orsino-Alain, there isn´t a lot of examples of circle mages. To be precise, Meredith has Cullen as second in command, and as good all around reasonable templar. Who is the second in command of Orsino, who is also reasonable and shows that not all mages are crazy? There is no one, unless you have circle Bethany. She also sents you a letter about the circle that gives another perspective about it, in a game that is seriously lacking about it - you get Anders rants and some npc banter, and that is it.
4. Bethany gets her own harrowing and therefore becomes an overall better and more responsible mage, while a warden bethany won´t have a harrowing and will just focus on combat magic. I like that Bethany keeps her personality and does not do a 180, plus if you want mage freedom then you can always side with the mages at the ending, it still makes sense, and the motivation to protect your sister is a strong one to oppose meredith, much better than: "I barely know you Orsino nor any of your mages, in fact i never set foot inside the circle, but i am risking my life for you anyway"..