You're grasping at straws.
The money they have exists entirely to pay Komachi. There is no other reason for the souls of the dead to have money. It corresponds to the assets of those that miss them--but that doesn't mean that it's other people's money.
Komachi, similarly, has absolutely no need for it. What, exactly, is a functionally immortal ferryman of the dead going to spend money on?
It looks symbolic: the more people that miss you in life, the more money you have, the shorter your journey is. You pay the ferryman for passage with the money you have that exists entirely to pay the ferryman passage.
Eiki is annoyed with Komachi for slacking off, not for losing spirits in the river, so it's not something that's happening much, confusion or not.
Therefore, 'evil' is stretching it, and deciding that shinigami, part of the natural order of life--because seriously, that's exactly what they exist for--are therefore embodiments of evil is just plain ridiculous.
But whatever, this argument obviously isn't worth it.
You can count the likely evil things in Touhou on one hand--Mima and Yuuka probably are, then there's the Saigyou Ayakashi, which has no particular reason for killing people other than it can. Could possibly fit Rukia in if 'diet consists of people' equals 'inherently evil' when it's not human to start with. :/