What to do when scriptures go against conscience?
Sri Krishnaprem, the great Gaudiya Vaishnava saint ( https://en.m.wikipedia.org/wiki/Krishna_Prem) writes in His 'Cruelty and Religion'
However divine the ShAstras may have been in its origin, it has been transmitted to us through the memories and writings of purely human beings who like all human beings are subject to error...There are many other practices which..are..intolerable cruelties...If we once admit the principle that Bhagavan would never sanction,let alone command cruelty, we must then fearlessly erase from our religions teachings of all such acts however well-established they may be.(The Search For Truth, page 115-6).
Krishnaprem further writes
Does the Lord of all sanction the cruelty or not?.. The Upanishads, the Gita, the Bhagawata, the Mahabharata are filled throughout with teachings setting forth in unmistakable terms the duty of love and compassion to all beings and thses lofty teachings, the crest jewel of the Sanatana Dharma, should be allowed to overrule by divine right all lesser or narrower teachings.Do not fear that the whole structure of Hindu religion will be weakened by such criticism. The Sanatana Dharma is no decayed house that will crumble to pieces at a touch. It is built of the rock of Eternal Truth and its sublime beauty will only shine out more replendently than ever if the mud plaster with which selfish men have covered it up be removed...MA hinsyAt sarvabhutAni--"Do injury to no living being!" This is subtle teaching of the Veda.
MahAjano yena gatah sa panthAh--I think He answered your question.
Please see how contradictory the sayings of our Smriti-s are regarding the age of marriage of a girl with the evidence avalable in our epics and puranas.The Baudhayana, Gautama, Vasistha or Parashara Smriti-s all recommend marriage before her reaching puberty! And what do we see in our Ramayana, Mahabhara and the Puranas? Was Sita or Parvati or Draupadi or Damayanti or any such female character got married 'while running nacked' as advised by the Smriti-s? No. They were matured enough and chose or being chosen by their husbands themselves. The Swayamvara obviously was never held for a girl who does not understand the meaning of marriage! I think it makes it clear that no such injunction existed originally, which leads to a conclusion that all these slokas of the Smriti-s recommending child marriage are interpolations of some later time when this was somehow needed by the society.
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