Context is needed for this. From the visual novel, the line is from Shiro, about surviving wounds that would otherwise be fatal if Avalon had not been inside of him. So when Avalon is removed Shiro remarks that things are the way the should be now (people dying, when you kill them.).
In this context, the phrase makes sense. When made out of context, it does seem silly.
Furthermore, following said phrase, Shiro says "それが当たり前なんだ", which more or less means, "that's only natural."
Official dub goes with something like: "when people are hurt badly enough, they die."
Furthermore in Japanese, there are two ways to describe death, one for body and one for soul. So you may kill one's body, but their spirit wouldn't may still persist. This is where the phrases like "he won't die, even if he is killed" probably originated from.