Lord Siva's punishment was just like that of a cowherd boy, who keeps a stick to frighten his animals. It is commonly said that to give protection to animals, a stick is needed because animals cannot reason and argue
SB Canto 4
My dear great and powerful Lord Śiva, you were created first from the mouth of Lord Brahmā in order to protect the brāhmaṇas in pursuing education, austerities, vows and self-realization. As protector of the brāhmaṇas, you always protect the regulative principles they follow, just as a cowherd boy keeps a stick in his hand to give protection to the cows.
The specific function of a human being in society, irrespective of his social status, is to practice control of the mind and senses by observing the regulative principles enjoined in the Vedic śāstras. Lord Śiva is called paśupati because he protects the living entities in their developed consciousness so that they may follow the Vedic system of varṇa and āśrama. The word paśu refers to the animal as well as to the human entity. It is stated here that Lord Śiva is always interested in protecting the animals and the animalistic living entities, who are not very advanced in the spiritual sense. It is also stated that the brāhmaṇas are produced from the mouth of the Supreme Lord. We should always remember that Lord Śiva is being addressed as the representative of the Supreme Lord, Viṣṇu. In the Vedic literature it is described that the brāhmaṇas are born from the mouth of the universal form of Viṣṇu, the kṣatriyas are born from His arms, the vaiśyas from His abdomen or waist, and the śūdras from His legs. In the formation of a body, the head is the principal factor. The brāhmaṇas are born from the mouth of the Supreme Personality of Godhead in order to accept charity for worship of Viṣṇu and to spread Vedic knowledge. Lord Śiva is known as paśupati, the protector of the brāhmaṇas and other living entities. He protects them from the attacks of non-brāhmaṇas, or uncultured persons who are against the self-realization process.
Another feature of this word is that persons who are simply attached to the ritualistic portion of the Vedas and do not understand the situation of the Supreme Personality of Godhead are not any more advanced than animals. In the beginning of Śrīmad-Bhāgavatam it is confirmed that even though one performs the rituals of the Vedas, if he does not develop a sense of Kṛṣṇa consciousness, then all his labor in performing Vedic rituals is considered to be simply a waste of time. Lord Śiva's aim in destroying the Dakṣa yajña was to punish Dakṣa because by neglecting him (Lord Śiva), Dakṣa was committing a great offense. Lord Śiva's punishment was just like that of a cowherd boy, who keeps a stick to frighten his animals. It is commonly said that to give protection to animals, a stick is needed because animals cannot reason and argue. Their reasoning and argument is argumentum ad baculum; unless there is a rod, they do not obey. Force is required for the animalistic class of men, whereas those who are advanced are convinced by reasons, arguments and scriptural authority. Persons who are simply attached to Vedic rituals, without further advancement of devotional service, or Kṛṣṇa consciousness, are almost like animals, and Lord Śiva is in charge of giving them protection and sometimes punishing them, as he punished Dakṣa.