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Here we have a person who alone could destory the world (via slaughtering hollows).
When you consider that 1 Menos is the equivalent of 100's maybe even thousands of hollows.
SS had already tried to wipe them out once, Ishida's grand father and father it seems got away by agreeing to not do Quincy shit anymore.
Now Ishida comes along and and starts killing Hollows left and right straight infront of Rukia's eyes. This should have been enough to get him killed by SS.
He then goes to SS making himself an easy target, still left alone even after being captured.
What makes things worse is that he KNOWS all this, knows that every hollow his kills can upset the balance of the universe and kill everyone, so what does he do next.... Goto HC with enough power to take out Meno's with ease increasing the damage done per kill exponentially. Why on earth wasn't he killed by Urahara nevermind allowed to go there
Fact of the matter, Ishida needs to die alone side all the other Steinrichters(sp) for the sake of all who live and arn't living but might live again!
Ishida's grandfather, Souken, was still a Quincy, when he was attacked by Hollow and died. I don't think a couple of Quincy killing Hollows makes such a big difference. Ishida isn't Superman, after all and SS doesn't care about the souls in that sense, but about the balance in general.
The conflict ended with a wipe out before, but the persistence of the Quincy also led to that war, and Ishida seemingly didn't have any killer against Shinigami, despite his grudge. He spared Kamaitachi's life, when he could have easily killed him. The only time he actually wanted to hurt a Shinigami was against Mayuri for known personal reasons.
Other than that, Ishida, although seemingly cushioning himself from the Shinigami matters, didn't act in a way to be a threat to the Shinigami. Even Mayuri in HM tended to his injuries and we all know his personality.
So, I don't think he's the bad guy in the town.
SS has changed. Mayuri said to Yamamoto the classic "I told you..." regarding Ishida & quincies in general, but was ignored.
Presumably SS didn't deem one lone Quincy to be any threat to the Balance of Souls. In fact, they had Ishida helping to clean up Hollows in Karakura town while Ichigo was out of action, so it seems they're not even too bothered about a few dozen Hollow spirits being completely erased from existence. That last bit strikes me as kind of odd. It's not like SS had any shortage of Shinigami to deploy to Karakura before the Vandenreich's massacre, so it seems that at the very least they should have forced Ishida to stop slaying Hollows. Those souls he's killed are forever gone now.
I don't think a lone menos counts as thousands of souls. We know menos eat souls however that does not in itself means that every soul devoured by a menos remains there. Imagine the result of the espada going to FKT if that was the case. The human world would have had to deal with god knows how many thousands of souls in just a second. Wonderweiss and furar would have made the entire situation even worst. In this regard a hollow would just devour the spirit particles of a hollow however the hollow's soul would not become a part of the hollow that devoured it, it would just die.
Don't forget what happened to Yama after he exterminated the Quincy 1000 years ago: He grew to want to protect humans.
Since Quincy like Ishida are human he was led by guilt to not do anything to Ishida.