In the Dragon Age series alone;
Alistair: yes, goody two shoes. Only time he gets really angry is about Loghain and Isolde.
Morrigan: hardly a paragon of virtue, and can get downright petty and evil sometimes.
Leliana: Cold blooded murderer. Her Chantry stance is also very much grey. Not a goodie two shoes.
Sten: Murdered an entire family, and has a generally very pragmatic and utilitarian approach. Neutral at best.
Shale: only really wants to squish things. Neutral.
Zevran: another murderer, and a very unapologic one at that. Again, neutral at best.
Wynne: Kinda like Alistair, kinda goody two shoes.
Oghren: brags about killing people, doesn,t care about much other than getting drunk and killing Darkspawn.
Loghain: straight up villain for most of the game.
Dog: he's a dog.
So that's two companions that are goody two shoes. All the rest are neutral, and some (Morrigan, Zevran, Loghain, Sten) could be considered outright evil by some. So that's not an argument.
For DAII:
Carver: Bit of a jerk, not many people like him. Willing to join the Templars, which does not indicate a goody two shoes personality.
Bethany: definitely sweet and nice.
Aveline: protect and serve, and all that. Definitely the most moral character.
Varric: Hawke's BFF, but he's no angel, he's a criminal who has killed more than his fair share of people. He's more white than dark, but definitely lots of grey.
Isabela: Self-centered pirate. She's not evil, but she's not a good person and unless Hawke convinces her she's perfectly OK with letting the Qunari burn Kirkwall if it means getting away with her skin intact.
Fenris: Vengeful and doesn't hesitate to kill people if he feels he has to. He has a sympathetic backstory but he's definitely in the grey area at best.
Merril: Yes, yes, sweet antics and all, she's still a blood mage who makes deals with demons to get what she wants.
Anders: Arguably one of the game's main villains, who kills innocent people to get what he wants.
Sebastian: Bit of a goody two shoes, but he can easily set his morals aside if it fits him (like if you let Anders live).
So that's two companion that's really moral, two lighter shades of grey, and all the rest are darker shades who could be seen as evil depending on point of view.
So with all that taken into account, I'm really not afraid. Most of the serie's companions are in the grey area, often quite dark. I don't see why Inquisition should be different.