I find it rather disturbing that someone should "prove that they are worthy of freedom". Freedom is not a "noble ideal" like Fenris says, it is one of our fundamental human rights. It doesn't matter that you think I am potentially dangerous, I have the right to be free and I don't have to prove anything to you. In a trial, it's the prosecution that has the burden of proof, not the defense.
Humans as we know them do not have the power to light cities on fire, with or without trying.
If we did, then "fundamental human rights" would look very different than what we know them to be now.
And, quite a few mages recognize this.
Plus, did you actually pay attention to what Fiona and Alexius say during the dialogue with the Inquisitor? The monarchy of Ferelden gave Redcliffe to the rebel mages as a safe sanctuary, but the Templars pursued them even across the border and were about to attack them. Fiona was terrified to see her fellow mages slaughtered by the Templars, that's why she resorted to an alliance with the magisters from Tevinter. It is even reported on the DA wiki if you want to check it out by yourself. It is called self-defense. If someone is attacking you, you're risking your life, and you find a knife lying around and use it to defend yourself, it doesn't matter if you wound of even kill your assailant. It is self-defense. It doesn't make you a murderer.
Not to mention that Fiona decided to ally with Alexius, not all the rebel mages. On the contrary, if you speak to them, for the most part they disapprove of this decision. But for all their life they have been subjected to an authority who told them what to do and when to do it, how can you expect them to suddenly be all autonomous and determined? It's obvious they will follow Fiona, who was First Enchanter and leads them by default.
Can we note the huge double-standard at work here? When mages follow bad orders/leaders, well, please do not think badly of them they were just in a bad situation and only the leadership need be blamed. When Templars do the same, hah, see how bad they are?! All of them must be cracked down on!
If the first thing mages do with their freedom is blindly follow a bad leader, why should anyone want them free? What choice did they have, you ask? What choice do Templars have? If they disobey orders, they likely get thrown in a military tribunal and severely punished. If they'd followed the order, they may still be free afterwards. If Templars should accept that consequence, what is the mages' excuse? Not like anyone is going to arrest them for defecting. Hell, they even have a choice of leader! Vivienne may not reflect all their views, but she won't lead them into hopeless war and force you to choose between death and Tevinter slavery.
Perhaps they should have thought this out better before they decided to recklessly break away from the Chantry. If their freedom was worth dying for in the first place, then they should accept the fate they chose for themselves rather than ally with Tevinter. If it was not, they should not have broken away.