There is a bit of a grey area here, but 'by' indicates the actual agent of the action and 'with' indicates the tool, etc. In the first, the person cut the bread more than the knife and in the second, the person threw the grenade, but the grenade was more active in the killing. If the person had thrown a stone and killed him, then you could say 'with'. However, different people may use these differently.
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