You only have to look at around 99% of all the plot points in the Dragon Age games to see the dangers of magic.
Do we, now? Let's take a look.
DAO
Broken Circle: Yes, admittedly, this one counts. (1)
Arl of Redcliffe: Also counts, though I would say the fear of magic is responsible for a third of this (magic itself is the second third, with the final third being the assassination plot that kicked everything off). (2)
Urn of Sacred Ashes: Nope, the magic here is rather benign. (-1)
Nature of the Beast: Not really about the dangers of magic, per se, so much as it is one mage being a dick. Nothing's really breaking out of control here. Maybe it's half a point. (2.5)
A Paragon of Her Kind: No magic involved here, aside from indirect enchantmenty stuff that can't go out of control. (-2)
The Landsmeet and associated quests: Definitely not. (-3)
The darkspawn: Unknown! As the Blight definitely predates the breach into the Black City (pre-Memories blighted lyrium), and we have evidence that it may have been unleashed by Andruil, it has by no means been satisfactorily proven that the darkspawn were created by magic used in a world resembling ours in any way. (0)
And for companion quests?
Alistair's Family: No. (-4)
Flemeth's Real Grimoire: Not directly, now that we know that possession wasn't intended to be harmful. (-5)
Leliana's Past: No.(-6)
The Sword of the Beresaad: No. (-7)
Wynne's Regret: No. (-8)
All the Crow stuff with Zevran: No. (-9)
Oghren's Old Flame: No. (-10)
A Golem's Memories: No. (-11)
Hmm. Awakening?
Velanna's shenanigans: She was doing damage with magic, but in this case, was basically just into violent banditry, so another half point. (3)
Sigrun's quest and Kal-Hirol: No. (-12)
The Blackmarsh mess: Yes! (4)
The Architect and all he tried to do: Kind of? It seems like his plan involved more alchemy than magic, though, so counting it seems shaky. (0)
Golems of Amgarrak and Witch Hunt... the former, somewhat, the latter not so much. (5, -13)
Let's move on to DA2!
Kirkwall's refugee crisis: Laughably no. (-14)
Birthright: No. (-15)
The Way It Should Be: No. (-16)
Long Way Home: No, unless fighting through undead mooks hanging out on Sundermount counts. (-17)
Tranquility: No; in fact, this is about the dangers of templars. (-18)
Fools Rush In: No. (-19)
Bait and Switch: No. (-20)
Wayward Son: It does come up in passing, I will admit. (6)
Blackpowder Promise: No. (-21)
Enemies Among Us: Yes. (7)
Duty: No. (8)
Shepherding Wolves: No. (-22)
Act of Mercy: No. (-23)
The Deep Roads Expedition: Yes, assuming you count red lyrium as such. (9)
Night Terrors: Yes. (10)
Repentance: Yes. (11)
Dissent: Yes, at the end with Justice. (12)
A Bitter Pill: No. (-24)
Blackpowder Courtesy: No. (-25)
Offered and Lost: No. (-26)
Mirror Image: Tangentially, depending on how magical you consider the varterral to be. (0)
Family Matter: Yes. (13)
The Long Road: No. (-27)
Prime Suspect: Almost, but not quite. (-28)
All That Remains: Yes. (14)
Following the Qun: No. (-29)
To Catch a Thief: No. (-30)
Demands of the Qun: No. (-31)
On the Loose: Yes. (15)
Alone: No. (-32)
Faith: No. (-33)
Justice: Belatedly, yes. (16)
A New Path: Yes. (17)
No Rest for the Wicked: No. (-34)
Favor and Fault: No. (-35)
Haunted: Yes. (18)
Best Served Cold: Kind of, at the end. (19)
The Last Straw: Half of it, yes. (20)
Then we have Legacy, which can be counted as a yes, and Mark of the Assassin, which is a no. (21, -36)
Near the end now! Inquisition!
The Wrath of Heaven: Yes. (22)
The Threat Remains: No. (-37)
In Hushed Whispers/Champions of the Just: Yes. (23)
In Your Heart Shall Burn: No. (-38)
The Verchiel March: No. (-39)
Promise of Destruction: No. (-40)
Last Resort of Good Men: No. (-41)
All New, Faded for Her: I'll count this as a no, since it's about the danger that humans pose to spirits. (-42)
Of Somewhat Fallen Fortune: No. (-43)
Here Lies the Abyss: Yes. (24)
Subjected to His Will: No. (-44)
Well, ****: Yes. (25)
Perseverance: No. (-45)
Wicked Eyes and Wicked Hearts: No. (-46)
Bring Me the Heart of Snow White: No. (-47)
Demands of the Qun: No. (-48)
Revelations: No. (-49)
The Left Hand of the Divine: No. (-50)
What Pride Had Wrought: I'd say no, though it could be argued yes. (0)
Doom Upon All the World: Yes. (26)
Which leaves us with Jaws of Hakkon as yes, The Descent as no, and Trespasser as yes. (28, -51)
So, with my count of the main quests, companion quests, and major DLC quests as plot points... our answer is that the dangers of magic make up approximately 35% of the plot points in the Dragon Age games. You might dispute some of my designations, but it's not over half, and it's definitely not 99%.