As has already been pointed out, they didn't give the player the choice to kill her, she chose to confront you herself and leading it into a fight which ended up with her knocked out, no matter what the cinema scene says.
It's not the "choice" that has most people worried, or at least not me. It was the consequences, evidence and the retcon. We saw her die. The codex was updated to... "When The Warden corrupted and destroyed the Sacred Ashes of Andraste, Leliana drew her weapon and was killed alongside the guardian." No matter what they say now, I do not believe that the original intention was for Leliana to survive. We were given consequences and they have been altered.
Contrast that to the video of the cowardly Hawke and the cunning Isabela (first time I have seen that). The player is told pretty much immediately that Isabela escaped. It is completely plausible and in character. It was what the writers always intended, there was no retcon. They showed you the consequences with Isabela warning Hawke that she will be back.
I'm not saying retcons are completely bad. Although they should in general be avoided, sometimes they are worth it if they are important enough to the story. From the DA2 perspective, Leliana was nowhere near important enough to justify it. However it does seem that in the greater scheme of things, including Inquisition, that she has a bigger and more important role. If the writers feel that her character is the perfect fit then I am ok with it.