Sure you can. It's one of the defining frustrations of insurgency warfare- conventional victory in the field does not always translate into political victory.
The Templars have the unfortunate objective of needing a political victory to achieve their war aims. Killing all the rebel mages in Southern Thedas doesn't end the mage problem. Even if they did conduct a total genocide (which they weren't aiming for- the war was not over or cast as a 'let's Annul everyone, right now'), the more mages will be born in the future.
Templar victory comes with the re-establishment of the Circles with acceptable oversight (which means oversight by Templars).
If the Templars no longer exist, that's a problem and they lose- they can't enforce the Circles, or even train replacement Templars. So a Templar conventional defeat and getting killed off is a pretty big deal to them. But it's not the same for the mages- more mages will be born regardless, because mages are a biology and not a polity. Templars are a polity, and it's all but impossible to resurrect a polity if it's killed.
But conventional defeat to the Mages isn't the only way the Templars could cease to be. The Templars could also be defeated by another military power- like the country of Ferelden, which would have both reason and ability to do so if the Templars sacked a major Ferelden settlement to kill a bunch of rebel mages. Which, again, wouldn't actually win them the war even if those mages were the last Rebel Mages in Southern Thedas, because 'victory' depends on what comes after the current rebellion is suppressed.
If the Templars attack Redcliffe but are wiped out in the counter-attack, they lose. And if the Templars ignore the peace appeals of the highest moral authority in Southern Thedas and massacre a bunch of (mundane and magical) good Andrastians even as the Mages appear to be playing reasonable... well, there's a high chance they'd lose the public support and tolerance they have, be unable to support themselves in the long-term even if they escaped Ferelden's wrath, and then they'd still lose. Again. And, really, the Templars are kind of going to need the Chantry in the long-term if they're going to re-set up the Circles, since the Chantry is what makes it all run smoother across the countries. The Templars have had enough legitimacy and public/private support to keep up a war for a few years, sort of like how the Inquisition manages, but that's not a long-term reliable solution. Without which, they'd lose. Still again.
No matter how much the Templars win in the field, they're pretty close to losing if they disregard politics. And that's a big advantage for the Mages. For the Templars to win, the mages need to accept that they've lost. If they're stubborn enough to hang on until the Templars screw up, then it's the Mages' win.
So for the Templars to win, they really need something like the Conclave anyway- something that's big and pretty and in which the Mages effectively surrender and return to the Circles. Since the alternative to the Mages returning to the Circle is the Mages not returning to the Circles, which amounts to the Templars losing, a little compromise is perfectly reasonable for the overall victory- as long as it's on terms acceptable to the Templars. The biggest two, I'd expect, being the replacement of the Divine they don't trust and feel betrayed by, and the end of the Chantry's indulgence/tolerance of the nakedly separatist Libertarian fraternity that led the revolt. The first could be won in the field if they killed the mages, but the second is almost entirely a political concession to be wrested in negotiations. How much is peace worth to Justinia- enough to 'retire' and let a pro-Templar Divine replace her?
Now, this isn't to say the outcome of the battles isn't important. It is. If the the mages are able to stay in the field because they can't be defeated, then they have far less reason to come to the table or make any concessions. Until a national authority decided to force them, they could keep all the freedom and independence they'd successfully gotten as long as they wanted. The Rebel Mages don't need a conventional victory to keep a hold of their independence- they just need to not lose. Even if they're at a stalemate, the fact that they are entirely autonomous and self-supporting makes it their win for as long as they keep it that way.
Sure, there are reasons they would want a peace deal- war weariness, or exasperating the political tolerance of the kingdoms they're holing up in. But these are relatively minor things, and not worth making huge concessions that would invalidate the international crisis they were willing to start in the first place. For the freedom fighters and instigators who are the energy behind the rebellion, the point of any peace deal is to preserve their victory. But if that was the case, then the pro-Independence faction would be at its height, not its lowest- they wouldn't leave their own champion and acknowledged leader behind.
In fact, in this context the biggest reason the Mages would have to go along with the Conclave is if their nest egg of the future generation was at risk. If their rear elements, their children and wounded and weak and their Tranquil, if all of them were at a risk the Mages couldn't stalemate if they weren't being protected by the walls of Redcliffe. That's a reason to go along and listen to the peace talks, if only to show a good face.
In this context, Ferelden is silently blackmailing the Mages by holding their refugees hostage. Which, I think we can all agree, would be rather out of character for both Alistair (who is good and sympathetic to the mages) and Anora (who may not be, but who likely wouldn't risk her own towns being turned into warzones if the Mages don't play ball).
On the other hand... if the mages aren't doing so well on the field, then negotiations take a different tone. It really is about survival or submission. If the Templars are frightening enough that the Mages don't think they could survive in the field, then they'll need an outside supporter to protect them- someone with the power and credibility and legitimacy to stand on their behalf. Someone like, say, the Kingdom of Ferelden offering refuge.
Now, security patrons don't work for free. If you want people to fight and protect you, you have to give them a reason to want to. That may mean compromises you would prefer not to- like, say, slavery and exile to an oppressive and exploitative mageocracy that devours even its own mages. Or, since this is Ferelden we're talking about and not yet Tevinter, listening to them when they say that you should really look at stopping the fighting that you're already losing. That if you don't, then they won't let you hide behind their walls and instead you'll be out in the field and with those mean, scarry Templars, but if you do then they'll make sure that things aren't so bad.
In this case, leaving your own leader and figure of the independence movement behind when you go to negotiations make a good deal more sense. Because you're already compromising to gain a security patron, the question of 'submission or extinction' has already been answered: the question is on what terms do the mages have oversight? The worse the mages have handled themselves off the field, the less leverage they'll have to resist. The worse the mages have handled themselves on the field, the less ability they'll have to resist- they'll be more dependent on the security patron, make more compromises to ensure their survival, and go along with worse terms.
In this context, Ferelden is the security patron that's bringing the Mages to the table in exchange for protecting them. This, I think most people can agree, would be far more in character for Alistair and Anora. Yes, it is the Chantry that's the face of the negotiations- but that's not surprising or a disproof. The Ferelden Monarchy, despite the assertions of some pro-mage Alistair fans, are on good terms with the Chantry despite disagreements on specifics. And the Mage-Templar issue is an international issue, not just a Ferelden issue, and de-nationalizing it and working through the Chantry is one of the defining hallmarks of the international Circle system. Ferelden's role may be quiet, but it would be expected to be.
This would also be quite in character with the mage rebellion we've seen as identified with Fiona. People hate it, but even arch-independence advocate Fiona went along with far worse when the Templars were decapitated and disorganized and the Chantry was so divided it couldn't even muster a voice to ostracize the Inquisitor, let alone publicly blame the Mages. Obviously Fiona herself isn't doing the negotiation, but Fiona's second greatest tendency as a leader after advocating independence is to be suspectable to pressure, direct and indirect. The fact that the first isn't feasible if the war is going badly is a reason why her fellow mages would have left her behind- the second is why even a benevolent security patron could have pushed her to agree to peace talks in the first place.
Simple enough?