In a deleted scene from season one, the group returned to the Vatos to seek shelter for the night but arrived to find everyone in the building had been slaughtered and walkers had invaded the area. Upon seeing the bloody corpses littering the hallways, Sophia couldn’t keep quiet, too distressed and upset to stop her whimpers.
The group didn’t know how extensive the infestation of walkers was or if there were any survivors around; stealth and silence were their only strengths. Daryl did not respond gently to the little girl’s fears, telling her to ‘put a sock in it’ and something that, to me, sounded like ‘we don’t have time for this crap.’
Carol immediately became protective of her daughter, cradling Sophia away from the sight of the bodies, trying to comfort her, and snapping at Daryl to leave Sophia alone. It was the first time we saw Carol be assertive in any situation, coming out of her meek and feeble shell to protect her daughter.
Daryl was unfazed by that and threatened to ‘shut her up or I will.’ Whether or not he would have followed up on that threat was left uncertain, as Lori stepped in to make him back off. Seeing that no one else was on his side in the matter, Daryl didn’t push it further. Subsequently, Sophia quieted.
Considering how little we knew these characters at that point, Daryl’s threatening statement could have very well meant he would have physically covered her mouth and pinned her down to ‘shut her up.’ However, understanding what we understand about Daryl now, I think his threat was more along the lines of glaring at the little girl until he pretty much intimidated her into silence, made her fear of him greater than the fear of the death around them.
It would not have made her feel better or comforted her, thus allowing her to calm herself and quiet down naturally, but it would have effectively put her in a petrified silence. To Daryl, it was whatever got the job done. To him, the situation was clear: nut up and shut up or we die.
There wasn’t time to be comforting and gentle; Season One Daryl wouldn’t have known how to be those things anyway, and the situation demanded that they keep as low a profile as possible. There wasn’t time to be afraid and traumatized. Plus, Daryl presumably grew up around hunters and the blood and guts of animals. True, it’s different when it’s human blood and guts, but he couldn’t relate to a child being afraid of those things. They were dead and down; be more afraid of the dead and walking.
After they organized a sweep of the building, Carol took Sophia aside and comforted her and gently got her to quiet down. This scene was deleted and the Vatos subplot was abandoned, but the interaction in it would have added more backstory as to why Sophia was so leery of Daryl in the opening of “What Lies Ahead.”