In Mods it's implied Shigure got killed by a car(accident).

But in re-reading it, Haru knows where to be to find Shiro and doesn't seem surprised that there's been an accident, either.

I think, if Haru had killed Shigure intentionally he wouldn't feel so much guilt. So, things must have been going fatally wrong somewhere.

Well considering in MODS it shows the past where he's talking about running away with Shiro I assume something happened where Haru mentioned it to someone or something and because of that he was killed instead being allowed to leave the group.