Yes I know, I remained silent in my first playthrough because I felt like she should do her job and then by the end of the game she got angry with me for some reason when I told her to let Jusitinia go.
As it is, telling her not to kill him actually delivers a nice piece of dialogue from the Herald, so I can live with it in other playthroughs.
I just don't see how the one has anything to do with the other; the two situations aren't remotely similar.
In the early one, we have a spy under the employ of the inquisition who has actively betrayed the inquisition by murdering another agent.
In her personal quest, we have a chantry sister Leliana used to be friends with but who is not and has never been under the employ of the inquisition, spying for a third party - not a hostile enemy - with no real implication that she meant active harm in this situation or that she would have been capable of harming either Leliana or the inquisitor if she tried. There's no trust to betray and no real threat posed.
And most importantly, in the early situation, the PC is not in a position to tell Leliana how to do her job. Leliana is one of the Inquisition's commanders, the Herald is just someone they keep around to close rifts and break deadlocks between them.
In the later situation, during her personal quest, we are the Inquisitor. We are the high command of the Inquisition. Leliana is our subordinate, sworn to follow our commands, however much leeway we give her in her job. If we tell her not to kill someone, she is disregarding a direct order. We could have been the most ruthless motherf*cker in Thedas up until this point, that doesn't matter; her job is to do as we say, not as we do.