In discussing these questions, we should keep in mind two important concepts that are easily forgotten. The first is that any government, cruel or otherwise, is made up of people, and only of people. It is not possible to hate a government and love the people who make up the government at the same time. Such a concept is absurd. It follows that, since Christ's teachings have their basis in love, the disciples of Christ could not hate the government. The appropriate question, therefore, is whether they considered them enemies who should be loved, as Christ instructed (Matthew 5:44). The answer is almost certainly yes, since the Romans were unclean Gentiles from another nation who trampled on God's Holy Land daily. Who could be a greater enemy to the Jews at that time?
The second forgettable concept is that at least a few of Jesus' disciples recognized that, as God's Son, He had a role in establishing Roman rule over His own people. Jesus Himself, having the fullness of the Godhead in Him (Colossians 2:9), set up the Roman government over Israel (Romans 13:1), and it was He who taught His followers to love their enemies.
Many Jews at the time of Christ's appearance on the earth may have recognized God's hand in setting up the Romans over Israel. Some probably assumed that He had allowed the Romans to take over because of sin, while others may have considered Him to have caused it, rather than simply allowing it. There were plenty of prophetic texts in their scriptures to support God's activity in setting up rulers to punish Israel. But the disciples lived with God in a very literal sense. They knew Him face-to-face and heard His teachings on love. They knew that He was asking them to love cruel people whom He himself had set up as their rulers.
They took this teaching to heart and applied it in surprising ways. Hear the words of the chief disciple, Peter, in 1 Peter 2:11-17:
Beloved, I beg you as sojourners and pilgrims, abstain from fleshly lusts which war against the soul, having your conduct honorable among the Gentiles, that when they speak against you as evildoers, they may, by your good works which they observe, glorify God in the day of visitation.These words of Peter hardly reflect the attitude of a man who is against the government. How could he feel the way he did, knowing the cruelty of the Romans? The answer is in the first part of the quote above: the honorable conduct and good works of the church among the Gentiles would cause them to glorify God. By the time Peter wrote these words, he had long since realized that Jesus' gospel message and His salvation were for Jews and Gentiles alike (Acts 11:15-18). While Peter's ministry was primarily to Jews in Jerusalem, he had daily interactions with Gentiles and probably saw Roman soldiers throughout the city every day. As he followed after Christ, he had a heart for reaching them as well as his Jewish brothers.
Therefore submit yourselves to every ordinance of man for the Lord’s sake, whether to the king as supreme, or to governors, as to those who are sent by him for the punishment of evildoers and for the praise of those who do good. For this is the will of God, that by doing good you may put to silence the ignorance of foolish men—as free, yet not using liberty as a cloak for vice, but as bondservants of God. Honor all people. Love the brotherhood. Fear God. Honor the king.
Although they taught a certain way of conducting ourselves in our daily behavior among nonbelievers, as Christ did, Peter and the other apostles said nothing about their inner desires concerning the continuation or discontinuation of Roman rule over Israel. Clearly they wanted the church to focus on the gospel of Christ and on living our lives in obedience to Him, for His glory. They probably assumed that Jewish converts to Christianity wished to no longer be under the thumb of the Romans, even while they subjected themselves under Gentile law. But there was no need to write about ending Roman rule in their letters to the churches. It was more profitable to encourage the brethren to love the Gentiles and to recognize that the Roman soldiers and rulers were God's ministers for good and for avenging evil (Romans 13:3-4).
There is a third concept we should keep in mind. It is possible to live a certain way, subjecting ourselves under man's law as the Bible instructs, and to simultaneously pray in a seemingly opposite way, asking God to end the cruelty of men in the government. This is a similar concept to one with which we are familiar: It is possible to love a sinner while hating the sin we see them do. Governments are made up of people, as I noted above. Jesus taught us to love our enemies, which allows for us to continue recognizing them as enemies while loving them in every possible way. Therefore, Jesus' disciples could follow every command of their Roman authorities and go far beyond what was asked (Matthew 5:39-41) while still considering them enemies. They could love the Romans with everything they had and still pray for the restoration of Israel as an independent nation. Whether this was actually a part of their prayer life is something we can't know for sure, but we can allow for the possibility.
But could they pray for the end of something that God Himself had established? Most certainly. There are several cases in the Bible of intercessory prayer by men of God for their people when God had decided to punish Israel. The prophet Jeremiah respectfully pointed out the evils he saw when God brought Babylon against Israel to punish her:
Look, the siege mounds! They have come to the city to take it; and the city has been given into the hand of the Chaldeans who fight against it, because of the sword and famine and pestilence. What You have spoken has happened; there You see it! (Jeremiah 32:24)The prophet Isaiah prayed an even more direct prayer when the evil deeds of Israel's Assyrian rulers grieved him:
Do not be furious, O LORD,Nor remember iniquity forever;Indeed, please look—we all are Your people!Your holy cities are a wilderness,Zion is a wilderness,Jerusalem a desolation.Our holy and beautiful temple,Where our fathers praised You,Is burned up with fire;And all our pleasant things are laid waste.Will You restrain Yourself because of these things, O LORD?Will You hold Your peace, and afflict us very severely? (Isaiah 64:9-12)
Paul pleaded three times for the removal of the thorn in his flesh, the messenger of Satan that he knew was from the Lord (2 Corinthians 12:7-8). In one of these three cases, God heard His servant and promised relief for a remnant of His people (Isaiah 65:8-10). But He told Jeremiah three times to stop praying for His people because of their evil (Jeremiah 7:16, 11:14, 14:11). He told Paul that His grace was sufficient because His strength is made perfect in weakness (2 Corinthians 12:9). But although God's answer was "No" in these two cases, there was nothing sinful, rebellious or offensive about the prayers offered. We cannot know God's answer until we ask Him the question.
Therefore, while Christ's disciples submitted to the law of the land as given by their cruel Roman superiors, even the cruelest of whom was God's minister, it would not have been sinful for them to privately ask God to remove the Roman government from their land so the people could enjoy more freedom. The disciples could love the governor while asking God to peacefully remove him from power. They could pray for blessings for the soldiers they encountered and then offer up prayers for the peaceful liberation of their people. It might not have been helpful to the church to offer such prayers publicly, and it is probably not helpful now. But there is nothing sinful about asking God to bring a peaceful end to a government that relies on force and violence to control its subjects, even though God has established that government and has commanded us to love the people who make it up.