The way I see it, innocence in that world is dead. Clem knows Lee is dead whether or not she shoots him. She will be emotionally scarred by it all the same, either way. The questions ISN'T what will least emotionally scar her. It won't make a difference. The logic behind making a noise is null and void because they are locked in, in case anyone missed that. And as far as wasting bullets, its not like she'd go walking through a field of walkers again. If she has zombie problems, she'll need more than what's in that one little clip, so one bullet won't make a difference. Avoiding them is and always has been the best way to deal with them. Plus, the argument is null due to the scene after the scene after the credits.
What's really matters is what kind of change you want Clem to make. And that depends on the kind of morals you crafted Lee with. It turns into what you wanted to teach Clem the entire time. Her innocence is gone, period. So what do you want for her? To be merciful? To be hopeful? What morals strike you as most important?
Believe it or not, at the end of the series, it's not about what you think is best for Clem. It's what you want Clem to think is best for herself.