It makes perfect sense to me. Leliana has no reason but to go along the track she's going down. The Inquisitor can either interject and make her question her choices or not. Sometimes it's completely chance encounters that can change us. Yes, telling her not to dispose of the traitor seems small and insignificant and easy to miss. But that's life sometimes. I kind of like it. But I can see how it might irritate some players. especially since we usually expect gameplay to go down a certain path. My experience is most gamers don't like games to reflect life.
That said, I don't see why it's a big deal unless you're only planning on playing through the game once. It's an element of the game that was surprising and unexpected. I'd take it as a good thing. Games would be boring if they did exactly what we expected them to.
What about the other moments you can make her question her choices? Like when you tell her her people are not disaposable? And all the times you give the "right" example by making non-ruthless decisions and judgments? Not only does all that not count, she ends up acting like none of it ever happened and you were in fact a ruthless assquisitor all along.
When you try to tell her to let it go, she suddenly becomes snippy and insulted, "How can you say that, after everything you've done?" when "everything I've done" was be kind and just and telling her not to be ruthless except for that one time I said nothing. So, yeah, her actions there were surprising, and not in a good way.