Zero tolerance is normally applied to not using common sense about school rule violations.
Why should there be something other than zero tolerance for actual criminal activity?
Because it shifts the decision about what should be punishable from the person with all of the information about the specific case, to a person with no information about the specific case - indeed, that person makes the decision before the case occurs, and therefore cannot possibly know the details.
Unless your law makers are omniscient clairvoyants, and can predict and enumerate every possible mitigating factor that could ever arise in any situation, this will inevitably lead to unexpected situations that are covered by the policy (or law), but which the maker of the policy (or law) would have exempted, had they thought of them.
For example: You make it a criminal offence, with a mandatory five year sentence, to tackle a stranger to the ground without provocation. A person is about to be hit from behind by flying debris, and a bystander saves his life by tackling him to the ground. In the absence of zero tolerance, the technical breach of the law is ignored for obvious reasons of common sense. With zero tolerance, the bystander serves five years in jail for his good deed.
It's a FUCKING STUPID idea, and is a perfect example of why it is vital to have a separation of powers - Lawmakers determine what is or is not lawful, but ONLY a judge can decide the penalty for a specific instance of illegality. In the above scenario, without zero tolerance, the cops can decide it would be silly to arrest the assailant; but if they make a poor call (perhaps unaware of the mitigating circumstances which are later revealed in court; or because they too have a foolish 'zero tolerance' policy), the judge can say 'You are technically guilty, but in the circumstances no punishment is warranted and you are free to go'.
Given the undeniable fact that the courtroom is the only place where all of the evidence and all of the circumstances of a given event are brought together for consideration, that is also the only place where it is possible to make a decision that takes account of all of that information.
It is very easy to be technically guilty of a crime, in circumstances where doing so is forgivable, or even laudable. In such cases, judges must have the power to be lenient. Legislators (or executives) should not be allowed to usurp that power.