The first time Nell shoots someone in self-defense, she just does. In one simple action, she took a life. There was no hesitation behind her pulling the trigger, because she knew it was her life or his. She had a shot, and she took it, like any good field agent would do.
That didn't mean there wasn't any guilt.
In the moments between her single gunshot and discovery in the bathroom, she had plenty of time to acquaint herself with the dead man at her feet, bleeding out from a wound she inflicted. In those minutes, all she could think about were the people that brought him into the world, and who this man really was. People don't appear in the world with the sole goal of killing, and all she can do is imagine the events that led to where he ended up.
It takes months, years even, and good therapy until she is able to look back on the incident without feeling some sense of remorse. She described her feelings to Nate once as regret, something he quickly sought an end to:
"Nell, the decision you made in those seconds saved your life. No matter what you feel now, after the fact, you had some feeling then, in the moment, that your actions weren't the best, but the best in the circumstance. Do not be sorry for, or regret, your continued existence."
At the time he explains that to her, all she can do is nod through red hair and tears, hoping that some day she will understand.
Before then, her world had to keep spinning. Her internal dilemma wouldn't stop the day-to-day, and regardless of inner turmoil, her life would be forced to continue.
Snapping out of it was never a permanent option - it was a temporary solution that was no substitute for years of reflection, contemplation, and realization.
Nell knows that if she goes into the field again, if something goes wrong, another incident could happen. The possibility is inevitable, and terrifying.
She never fully 'gets over', per say, her first shooting, but she learns to get past it.
Yet, the click of her gun's safety would sound in her dreams for years to come.