
Seeing someone get killed in front of you would be a traumatic situation for almost everyone, especially when it's done in such a violent way. It's only natural to be afraid of the person who did the killing, even when he did it to save you, since he reminds you of the situation and you saw him do something horrible. Hence why Seungjae covered his eyes. He knew this wasn't something he should've seen.
It doesn't matter that the people who died were dangerous and a threat to his life, it's still traumatic nonetheless and it only gets worse when you consider how much abuse he already had to endure in the past.
I think he isnt afraid of him. But he has been the target of abuse for so long he is afraid of the situation.
Like....when a dog that has been abused for so long finally gets rescued and goes to a good family. If they do something like accidently break a plate and swear or something...the dog gets scared very easily by it. Its not scared of the people...but by the sudden sound and situation.