Don't get me wrong. I know I push myself to be this staunch Mage supporter, but I actually support the Templars who have the mind mentality like Emeric.
So why do you find it so difficult to support the Chantry in the same manner when you have examples of them showing mages respect and trying to ride herd on the worst of their Templars? You acknowledge that some Templars are in fact trying to help you figure the Chantry has no hand in that either? It doesn't occur to you that seeing someone like Justina encouraging people to treat mages with honor and respect might not be a factor?
Even in Dragon age Inquisition, it's been noted that it's the Chantry (Not the Templars) that came together with the mages at the Temple of the sacred ashes for a peace conference.
You want to know why Elthina, Justine and the Chantry as a whole has to be careful HOW they handle the Templars? Why they can't just tell them to do whatever they want? Why they need the Mages to prove they can be trusted before being able to loosen restrictions? Because the Templar's true loyalty isn't to the Chantry, it's to their interpretation of the Maker's will.
Let's take a look at Sister Petrice since you do so love to bring her up. She honestly believed the Qun was a threat to the Maker, and that those who followed the Qun could be killed in the Makers name. So she goes around the Grand Cleric's back and attempts to engineer a situation that will lead to open war. Thankfully Hawke can bring the truth to light, and the Grand Cleric will immediately revoke Petrice's protection and hand her over to the authorities. The Templars have a similar relationship to the Chantry. Some of them will only follow the Chantry so long as they believe the Chantry is following the Makers will or doing the right and sensible thing. And before you go blaming the Chantry for teaching them to hate Mages, Lambert, the one who lead the charge to abandon the covenant was from the Imperial Chantry and believed that Mages could govern themselves....until his former friend and Mage proved differently.
If you've ever seen Deep Space 9, you'll recognize the relationship between the Maker, the Chantry and the Templars. It's not too dissimilar to that between the Changelings, Vorta, and Jem'Hadar. Both the Vorta and the Jem'hadar revere the Changelings as gods and are doing their best to serve them, but both sides disagree about the best ways to do that. Basically the Dominion is the evil totalitarian version of what you see in Dragon Age.
Anyways, the point is the Chantry has good people trying to help others, not just the mages, but the elves and other downtrodden as well. Most people still appear to look upon the Chantry with favor which makes them an excellent avenue for promoting change.
Which reminds me, I now know why *YOU* should support the Chantry. Since the Chantry's heads have likely been killed in the same explosion that killed your mage leaders, supporting the Chantry might allow you to influence the message. This is your chance to affect wider Change, to use the Chantry to promote your own view of how mages should be treated. Afterall, the Chantry was already leaning towards treating mages with respect, that's why the Templars left, so now you have the chance to keep that up, and encourage all of Thedas to treat mages as you want them to be treated.