I'm sorry, I really don't follow you. You said Leliana directly refers to one conversation? which one then? And how can she directly refer to it when she says I did the opposite of what I actually did?
I said that you can see it as such. What she says fits any of those 3 cases.
And how does "how you treat your people" affect Leliana directly? Only the specific conversations do, right?
Yes, I'm confused. I'm not "using" Leliana there.
Ok, I'll try to explain:
First of all the key here is Justinia who used Leliana as a tool, which in turn led Leliana to convince herself that this is how things are done, that people, herself included, are to be used as tools for greater good or whatever. This is clear, is it not?
The first opportunity to undo this is with the traitor, since the traitor is a tool his life does not matter, even more so since this tool didn't functioned properly. You stopping Leliana here tells her that his life matters. It doesn't matter that you have no authority at this point because your act tells Leliana who you are as a person and makes her reflect her own views on this matter, especially obvious if you go "if you dislike doing something, there is something wrong with what you are about to do" line.
Second opportunity comes after Haven, I think this one is more obvious. You outright tell her that your people matter to you. Another crack to her "people are tools" conviction.
Third and final opportunity comes with the sister. If you tell Leliana to kill her, you are essentially telling her "Leliana you are my tool, do what must be done". It's not about saving sister's life it's about telling Leliana that she is not a tool what matters here.
Adamant soldiers and Winter Palace imo also should have counted here, the first didn't probably because the devs were afraid that many would not find all soldiers, and the second probably because it would constrict the epilogue significantly.
Still confusing?