The system is designed to protect the innocent. That builds in a lot of checks to protect the guilty, so sometimes you have the issue of executing a fundamentally different person than you started with.
Is there a consensus on what 'a thought' even is? There seem to be a lot of assumptions in this idea that I'm not sure are justified, like that 'thoughts' are discreet, localized events in the brain and that mental energy is like a battery powering thoughts and not an affective state.