I know I've said it before, and I'm saying it again.
The underlings of both sides got duped and misled. Some say that the templar subordinates have more justification by virtue of being tricked by their leaders, but I say this is unequivocally false. Not them being duped, but the part where they have more justification than the mages.
Leading up to either quest, we have mages in Redcliff, 3/4 of them in fact denounce Tevinter and want to get away, practically begging the Inquisition to save them. Just today while doing my Cadash playthrough, I heard Connor debating with one of the Tevinter agents and outright dismiss him saying that Tevinter doesn't know what they're talking about. Lysas seems barely out of apprenticeship and is scared out of his mind, hoping beyond hope that the Inquisition will free them. That tranquil in the tavern talks about how many non-mages and most of the tranquil were evicted, along with anyone who could have resisted Alexius. We know from the locked door near Connor that the Tranquil were actually used to make the ocularum in secret. Then there was the mage who was in the tavern who was happy in the Circle but felt staying with Vivienne's group or the group outside the town would be a sure death sentence because the templars don't care about the details at present.
Once the Tevinter came, Fiona's idiocy, or being slightly nudged with blood magic the way Avernus did, or whatever the case is, ruined things for the rank and file of most mages. And we know later in the game that those who didn't escape and fall in line were killed, just like the templars. Or were outright brainwashed.
On the Tevinter side, templars have choices as well. That Grand Cleric we see in Val Royeaux, if we talk to her after she gets decked across the face, tells us that there are some templars who remained with the Chantry. We have Lysette and her templar friends in the Inquisition, feeling it is better to protect the people rather than go rogue, fight amongst themselves and make things worse for everyone. And then the recruits in Therinfall ARE taking Red Lyrium, and there is evidence to support that it isn't good for them. Changing behaviors among the upper ranks, Varic's tales of the Champion and the truth of what happened to Meredith three years earlier, and they can see the madness that is their leaders.
If they left or questioned their orders, they were dealt with, just like the mages.
But the one thing the templars have against them that the mages do not. They swore an oath, and each and every single one of them that left the Chantry has broken that oath knowingly. Whether they were just following orders, were intimidated by their superiors, or whatnot, it was a conscious decision each and every one of them made, whereas many mages had the war forced on them when the templars rebelled. The Human Inquisitor mage outright says it in the summary.
I find both sides rank and file getting the shaft thanks to the decisions of their leaders. Lysas said it today when I said "you sound like you have doubts" while speaking with him about whether or not the Inquisition can help. "They all blame mages. Why call it a mage rebellon when the templars are the ones rebelling? Their crime is worse since they swore an oath and we did not, our leaders forced us into this," or something along those lines.
Now, with that said, Barris is a really cool templar, and probably my favorite in the whole series. When he joins the Inquisition, he is the very epitome of the ideal templar. He's honorable, he cares about the mages, he cares about the common people, he questioned his orders in Val Royeaux and in the templar mission before it became apparent that templars loyal to the principles on which they were founded were being purged. And he goes out on missions for the Inquisition unlike Fiona who just hangs out.
It is my opinion that Barris makes the templars look more sympathetic because he's such a cool guy.