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I don't read the novels, but if I remember right, Kiritsugu was famous as the "mage hunter", he kills mages before breakfast.
As we know, mages, even the relatively good ones tend to not care about the lives of muggles, let alone the less-good ones. So, killing a mage could potentially save the life of more people, in the event that a mage went rogue and did some vile researches (if they hadn't already). The reason Tokiomi and the gang wanted to stop caster wasn't because they resented the atrocities he did, but rather because he did it too flashily.
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