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The Old Testament says that those who disobey parents should be put to death. How can I explain this? We do not do this today. Why is this commandment no longer in effect? Is it because Christ saved the adulterous woman from stoning, and so put an end to the death penalty? But at the same time, the Church supports the death penalty for murderers. Why death penalty for one and not the other, if both are mentioned in Old Testament?

The entire context of any biblical passage must be understood and evaluated precisely to ascertain the full message and accurate meaning, so the expected behavior can be applied accordingly. The Holy Book of Deuteronomy 21:18–21 addresses the provisions for ensuing justice in society that was designed as a theocracy in which God prepared and preserved His nation in anticipation of the Messiah, the Lord Jesus Christ. Death had been man's destiny since the fall of Adam, but through the abundance of God's grace, man's wounds are healed, and his life restored by the death and resurrection of Christ Jesus (Romans 5). 

Through God's mercy, due process was established to prevent brutality, abuse, and extremism. God designed a theocratic system in which He would interweave mercy with justice. Thus, the law demanded justice but also protected due process.

"If a man has two wives, one loved and the other unloved, and they have borne him children, both the loved and the unloved, and if the firstborn son is of her who is unloved, then it shall be, on the day he bequeaths his possessions to his sons, that he must not bestow firstborn status on the son of the loved wife in preference to the son of the unloved, the true firstborn. But he shall acknowledge the son of the unloved wife as the firstborn by giving him a double portion of all that he has, for he is the beginning of his strength; the right of the firstborn is his" (Deuteronomy 21:15–17).

Public trials were enforced to prevent overzealous parents and relatives from enforcing cruelty toward their children. Even in this patriarchal society, the father's power over his own child was limited, and human rights were safeguarded. The penalty of capital punishment was designed to execute convictions with a just sentence under stern requirements and the verification of multiple witnesses was mandatory (Deuteronomy 17:6). Christ's accusers—the chief priests and elders, also applied this rule but could not find credible witnesses to prosecute the Lord in a just manner that befits the law.

"Now the chief priests, the elders, and all the council sought false testimony against Jesus to put Him to death, but found none. Even though many false witnesses came forward, they found none. But at last two [c]false witnesses came forward 61 and said, 'This fellow said, ‘I am able to destroy the temple of God and to build it in three days.''" (Matthew 26:59–61). 

Disobeying one's parents is believed to be a vile manner of conduct. Children were to acquire blessings via their parents' approval. The death penalty—capital punishment, still applies in some countries and in some states. The Church does not oppose this law, but only agrees when all the evidence presented is without a reasonable doubt that the unremorseful perpetrator indeed committed a heinous crime, rejected all rules of the civil society, and is likely to commit further atrocities. The Church values life, but in these cases where capital punishment is the sentence, the accused person had abhorrently devalued the life of others and, thus, the just penalty is death. This process is not executed swiftly, but rather can take many years until all appeals are concluded. Therefore, there is ample time for the prisoner to repent and accept responsibility, and may even be forgiven by God. 

God illustrated His mercy to David, although David committed murder and adultery. Prior to divine intervention, St. Joseph extended mercy to the Virgin Mother by shielding her from public humiliation of being found with child while still betrothed (Matthew 1:20). The parable of the prodigal son conveys the depth of the father's heart that burned for his son's repentance. Sadly, it was his son that insisted on a miserable fate. Nonetheless, when he came to himself, he returned and was accepted by his father (Luke 15:11–32). God never ceases to yearn for our repentance. Thus, the man or woman, son or daughter, who were subjected to any form of capital punishment are convicted because of their vile, persistent, over-indulgent, immoral, callous behavior, and determination to infiltrate their wickedness on society with no remorse. 

Despite the punitive method to deter crass and vulgar behavior and corruption in society, God's mercies are evinced in the Old Testament by adding guidelines to limit excess. His mercies are not only plainly revealed in the New Testament, but He absorbed the curse and ultimate punishment of death on our behalf and fulfilled all the laws from the beginning even as He hung on the cross (1 John 2:2). The Lord Jesus Christ is just and merciful. Isaiah the Prophet revealed that Christ accepted our punishment as though He was the impure assailant deserving of death: "And the Lord has laid on Him the iniquity of us all" (Isaiah 53:6). We, as Christians, ought not to neglect prison ministries. In the passages below, the Lord Jesus Christ is not even referring to the imprisoned by derogatory terms, but rather puts them in the category of the least of His brethren, not because He loves them any less, but because they have been marginalized according to our perceptions and judgments: 

"Then the King will say to those on His right hand, 'Come, you blessed of My Father, inherit the kingdom prepared for you from the foundation of the world: for I was hungry and you gave Me food; I was thirsty and you gave Me drink; I was a stranger and you took Me in; I was naked and you clothed Me; I was sick and you visited Me; I was in prison and you came to Me.' Then the righteous will answer Him, saying, 'Lord, when did we see You hungry and feed You, or thirsty and give You drink? When did we see You a stranger and take You in, or naked and clothe You? Or when did we see You sick, or in prison, and come to You?' And the King will answer and say to them, 'Assuredly, I say to you, inasmuch as you did it to one of the least of these My brethren, you did it to Me.'" (Matthew 24:34-40).