If Balewin is considered to have violated the IR through mere threats then punishment must be given and Magistrates have the option to lock an account for between 1 to 3 days and locking is the only option we have. A warning is NOT a punishment.
A warning is indeed a "punishment". It is a confirmation that a rule was broken, a chastisement, and a reminder to not do so again.
Unless you are saying that the Magistrates cannot issue warnings. i.e. if the only options the Magistrate interface will let you choose are between a one day lock and a three day lock. If warnings and reprimands are not an option, I consider that a deficiency in the powers that the Magistrates have.
The wording in the IR leaves no leeway:
No, it does not allow any leeway
in determining what is and is not a violation. There are no ameliorating circumstances or "justifiable violations". Which is what that list you quoted talks about.
Whether he didn't mean it or it was not his intention to doesn't matter. It CANNOT prevent the punishment. Which means we would be wrong to only give a warning and while the form of punishment is not prescribed in the IR punishment must certainly be an action.
You are implying here that aggressive enforcement needs to include aggressive punishment. That is not the case. You can aggressively enforce the rules by not allowing rationalizations, extenuating circumstances, intent, and other such explanations for why some particular violation was not really a violation. By not allowing those types of things to distract from whether or not what was said is a violation. It does not require that any punishments dealt out are also aggressive and harsh.
And no - sending a (warning) message is NOT an action.
It most certainly is. Why else would you have the option to send one? After all, if the ruler was not broken, then why do you need a reprimand/warning? Keep in mind that the IRs don't allow "wiggle room". Either you broke the rule, or you didn't. And if you didn't break an IR, then nothing needs to be done. Including sending a message. Because how ridiculous would it be to send someone a private reprimand, or a public warning, and then in that reprimand/warning, tell them that they didn't do anything wrong?
