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Even though Luther found great abuses in the Church of his time, there is the clear idea in the Bible that the Church is one, Jesus even prays that his followers be in unity. ("I pray that they will all be one [...] " John 17:21)
So how did Luther justify separating from Rome?
Martin Luther had not intended to separate from the Catholic Church. His 95 theses, and his conduct immediately after he posted them, were intended to achieve reform in the Catholic Church. When he was excommunicated by Rome, he had to either give up his quest for reform or continue to pursue it outside the Catholic Church.
Bear in mind that there may never have been a single Christian Church, and there certainly was not just one Church in the time of Luther. We know from Paul's epistles that there were already divisions even in his own time, and of course we now know of the Gnostic Christians. Luther would have known of the Greek Orthodox Church, the Coptic Church and possibly even the Nestorian Church. Perhaps Matthew 16:18, in which Jesus says "... I will build my church", suggests that there should only be one church, although others may say that this is not the only possible interpretation of the passage when read in context.
Martin Luther justified his actions because he believed they were right, in the context of the Church in western Europe at the time he took those actions. If at any time in the future the Catholic Church wishes to reunite with the Protestant Churches, it is open to the Church to initiate dialogue with those Churches, but for this to succeed it must accept the possibility of genuine change both within and outside the Roman Catholic Church. Martin Luther would have welcomed any such action by the Catholic Church.
Here's how Luther describes his break from Rome taken from his Table Talk:
The chief cause that I fell out with the pope was this: the pope boasted that he was the head of the church, and condemned all that would not be under his power and authority; for he said, although Christ be the Head of the church, yet, notwithstanding, there must be a corporal head of the church upon earth. With this I could have been content, had he but taught the Gospel pure and clear, and not introduced human inventions and lies in its stead. Further, he took upon him power, rule, and authority over the Christian church, and over the Holy Scriptures, the Word of God; no man must presume to expound the Scriptures, but only he, and according to his ridiculous conceits; so that he made himself lord over the church, proclaiming her at the same time a powerful mother, and empress over the Scriptures, to which we must yield and be obedient; this was not to be endured. They who, against God’s Word, boast of the church’s authority, are mere idiots. The pope attributes more power to the church, which is begotten and born, than to the Word, which has begotten, conceived, and borne the church. We, through God’s grace, are not heretics, but schismatics, causing, indeed, separation and division, wherein we are not to blame, but our adversaries, who gave occasion thereto, because they remain not by God’s Word alone, which we have, hear, and follow. CCCCLIII. Table Talk, translated by William Hazlitt.
