Well she murdered for Justinia and she is venerated by every single person on Thedas. Thedas is too much of a dump to solve problems without violence. Actually Cass and Vivienne firmly rely on Inquisition to succeed and will ultimately fail without this support (high disapproval with Inquisitor). Leliana on the other hand does what she does with zero help from Inquisition and once she is done, she claims support for Inquisition.
Who do you think keeping the crows away from Inquisitor? You guessed right, Leliana.
Leliana was the Left hand and the ordinary citizens of Thedas know nothing about her actions, just like they don't know what she does for the IQ. Unless it's shouted from the roof tops and that wouldn't make her a very good spymaster.
Keep on thinking nobles, merchants, and everyone else will welcome the newfound competition and not blame the one who declared them free.
And yeah she keeps the crows off me, she's a good spymaster but even she admits that she has blind spots especially if doing more than her work. Something she tells you if you ask her to come with you. She also let Thom Rainier slip by. And that is my point about Leliana. She is good, but everyone makes mistakes and all it takes is one. I liked hardened Leliana, but there are only so many throats you can cut before someone is cutting yours.