Actually, from the way the conversation is going the whole "Death Squad" debacle can be interpreted as such,
- Zealot Templars go beyond the duty and start weeding out and purging associates of mages, whether they are blood mages or not; despite Meredith telling them not to do this
- Nobles hear or see this going on, and with Hawkes opposition to Meredith, assume that these "Death Squads" are some sort of retaliation on Meredith's part, and ask the Champion to stop them
Yeah, there is never any evidence that Meredith was behind anything and thanks to The Last Holdouts we know that Mettin is a blood crazy nutter that would kill anything holding a long stick. Or anyone standing near them.
Not exactly someone I would trust in performing something super controversial like murdering innocents as they stand in the streets in front of their neighbors.
In fact, I would like to point out that the "hidden supply cache" has more mercenaries in it than Templars and there is no evidence there of it being Templar owned/run at all. Those Templars could've simply been there to investigate a merc hideout but Hawke just shows up and slaughters them all.
Like I said, this quest was a poorly written mess.
I don't think any thought went into it other than "okay the Pro-Templar people have a quest killing blood mages... they have an option to kill/save some innocents and they have to decide which Templar to support."
"What about the pro-mage quest?"
"Oh I dunno. Meredith is bad. Kill Templars."