Another possibility is that maybe he knows it was her and he was happy that his onee-chan died. Maybe he was being abused or something.
There's also the fact that we still don't know how this Yakuza organization operates, and we're unaware of the parameters that dictate when Nezumi is ordered to carry out a hit.
I mean, I highly doubt the Yakuza would be like, "Nezumi, see that random ass civilian girl over there? Yeah, take her out."
So, we can speculate that she might have been involved in something dangerous, too.