every input to the system is important. Hormones generated by the sensation of hunger tip the balance of the yes/no classifier to make you more rash, or "cranky", because there's an evolutionary benefit to doing this in that it drives the whole system to seek food more urgently, for example. If you shut down the ability to feel crankiness, the system is no longer receiving proper input and is partially broken. Anger, passion, etc. are just how we understand a set of signals that actually have a deeper meaning. To simply neutralize anger out of hand (as opposed to calming down, where you strategically choose to reinforce alternative inputs in response to the anger), you would need to blank the entire set of inputs causing the "overload", discarding valuable information - such as your memory of what made you angry - along with it.
neurons are analogue and chemical in nature. As they operate, they change their responses to problems. It might be that they become overworked and need a rest, at which point they start to fritz; more significantly, the basic mechanism of learning is that neurons gradually rewrite both their connections to one another, and their decision function, according to the results of the last classification they made. So unlike a computer's logic gates, it is not possible for a neuron to reliably generate the same output to the same input time and time again. You cannot eliminate boredom, novelty, and so on, because they are fundamental to the basic operation of the system. At best, Evil Guy would permanently rob victims of the ability to learn or remember anything new (not just short-term, like Memento: their thoughts would be frozen forever).
corollary to the above: there is no deterministic mechanism available for the brain to use. When we work out symbolic logic or mathematical expressions, we're much slower than machines because we essentially have to consciously "simulate" a logical layer on top of this fundamentally different architecture, by imagining the "slots" for data and actively choosing to push numbers around (and many of us are bad at this). For a person to actually work completely logically, they'd have to be doing the equivalent of sums on paper to decide what to do next. For every action.
This is grossly oversimplified. Do not assume this is actually how the brain works (and whether neurons are responsible for all of it, or whether our understanding of them is complete, remains contentious). But the point is the same either way: logic and emotion are artificial constructs, neither of which fully reflects the way a human mind actually works (it is a kind of machine, and everything it does has a reason, but not a deterministic machine like the computers we build to do the jobs it can't). Logic and emotion are just post-hoc interpretations of a single deeper principle. Emotion can be described as the situation that arises when a wide set of inputs unify, and become as a driving issue for the whole system to make a choice about.