For lengthy historical and theological background information, see: Catholic Encyclopedia: "Monothelitism and Monothelites," written by John Chapman. Monothelitism was condemned as Christological heresy by the sixth ecumenical council at Constantinople, in 680-681. Pope Leo II confirmed (in 683) the conciliar decrees against the heresy.
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No earnest Christian wants to be considered a heretic. But we Protestants recognize Scripture alone as our ultimate rule of faith (the Reformation principle of sola scriptura). Therefore, we bring even the statements of Ecumenical Councils before the bar of Scripture. While one disagrees with the promulgations of an Ecumenical Council only with great hesitancy, nonetheless, since we do not regard these as invested with divine authority, we are open to the possibility that they have erred in places. It seems to me that in condemning Monotheletism as incompatible with Christian belief the Church did overstep its bounds.
Fair enough. I understand sola Scriptura and the Protestant conception of the rule of faith: as expressed above. I've written about it and debated it (by far) more times than anything else I have done. Dr. Craig did not, however (unfortunately and ironically), provide even a single Bible passage in his reply, to back up his case. If he appeals to the principle of sola Scriptura, it would seem sensible that he would try to produce at least some Scripture in favor of his position, since he specifically has appealed to Scripture over against ecumenical councils.
This is the classic Protestant approach: first exemplied by Martin Luther in his statements at the Diet of Worms in 1521: appealing to Scripture Alone and asserting that Church councils err and contradict each other.
If Dr. Craig and Protestants generally speaking "are open to the possibility that they [ecumenical councils] have erred in places," then presumably they should also be open to the possibility that their own biblical interpretations also could quite possibly err. I think this is one such instance. What does Scripture say in the first place, about it? The sola Scriptura Protestant gave no argument one way or the other from the Bible. But this Bible-loving, "biblical evidence-oriented" Catholic apologist thinks that Scripture has a great deal to say on the matter: and it entirely backs up infallible Catholic Christological tradition.
Jesus distinguishes His human will from His Divine Will, but completely subordinates the former to the latter. According to Ludwig Ott in Fundamentals of Catholic Dogma (p. 148), here are the scriptural proofs of the orthodox Catholic (and mainstream Protestant) position (with one or two of my own added):
Matthew 26:39 (RSV) And going a little farther he fell on his face and prayed, "My Father, if it be possible, let this cup pass from me; nevertheless, not as I will, but as thou wilt."
Luke 22:42 "Father, if thou art willing, remove this cup from me; nevertheless not my will, but thine, be done."
John 5:30 I can do nothing on my own authority; as I hear, I judge; and my judgment is just, because I seek not my own will but the will of him who sent me.
John 6:38 For I have come down from heaven, not to do my own will, but the will of him who sent me;
Other passages presuppose a human will:
John 4:34 Jesus said to them, "My food is to do the will of him who sent me, and to accomplish his work.
John 5:19 Jesus said to them, "Truly, truly, I say to you, the Son can do nothing of his own accord, but only what he sees the Father doing; for whatever he does, that the Son does likewise.
John 8:29 And he who sent me is with me; he has not left me alone, for I always do what is pleasing to him.
John 14:31 but I do as the Father has commanded me, so that the world may know that I love the Father.
Romans 5:19 For as by one man's disobedience many were made sinners, so by one man's obedience many will be made righteous.
Philippians 2:8 And being found in human form he humbled himself and became obedient unto death, even death on a cross.
Hebrews 10:9 then he added, "Lo, I have come to do thy will." . . .
The freedom of choice of Christ's human will is demonstrated:
John 10:18 No one takes it from me, but I lay it down of my own accord. I have power to lay it down, and I have power to take it again; this charge I have received from my Father."
Jesus conceptually distinguishes the Father's will from his own (these are all further proofs of my own, that Dr. Ott did not cite):
Matthew 7:21 "Not every one who says to me, 'Lord, Lord,' shall enter the kingdom of heaven, but he who does the will of my Father who is in heaven.
Matthew 12:50 For whoever does the will of my Father in heaven is my brother, and sister, and mother. (cf. Mk 3:35)
Matthew 18:14 So it is not the will of my Father who is in heaven that one of these little ones should perish.
John 6:39-40 and this is the will of him who sent me, that I should lose nothing of all that he has given me, but raise it up at the last day.  For this is the will of my Father, that every one who sees the Son and believes in him should have eternal life; and I will raise him up at the last day.
Many other passages show that Jesus' human will always agreed with His (and the Father's) Divine Will:
John 5:17 But Jesus answered them, "My Father is working still, and I am working."
John 8:28 So Jesus said, "When you have lifted up the Son of man, then you will know that I am he, and that I do nothing on my own authority but speak thus as the Father taught me.
John 10:28-30 and I give them eternal life, and they shall never perish, and no one shall snatch them out of my hand.  My Father, who has given them to me, is greater than all, and no one is able to snatch them out of the Father's hand.  I and the Father are one.
John 10:37-38 If I am not doing the works of my Father, then do not believe me;  but if I do them, even though you do not believe me, believe the works, that you may know and understand that the Father is in me and I am in the Father.
John 12:44-45 And Jesus cried out and said, "He who believes in me, believes not in me but in him who sent me.  And he who sees me sees him who sent me.
John 14:7-10 If you had known me, you would have known my Father also; henceforth you know him and have seen him."  Philip said to him, "Lord, show us the Father, and we shall be satisfied."  Jesus said to him, "Have I been with you so long, and yet you do not know me, Philip? He who has seen me has seen the Father; how can you say, `Show us the Father'?  Do you not believe that I am in the Father and the Father in me? The words that I say to you I do not speak on my own authority; but the Father who dwells in me does his works.
John 16:15 All that the Father has is mine; therefore I said that he will take what is mine and declare it to you.
Colossians 1:15-19 He is the image of the invisible God, the first-born of all creation;  for in him all things were created, in heaven and on earth, visible and invisible, whether thrones or dominions or principalities or authorities -- all things were created through him and for him.  He is before all things, and in him all things hold together.  He is the head of the body, the church; he is the beginning, the first-born from the dead, that in everything he might be pre-eminent.  For in him all the fulness of God was pleased to dwell,
Hebrews 1:2-3 but in these last days he has spoken to us by a Son, whom he appointed the heir of all things, through whom also he created the world.  He reflects the glory of God and bears the very stamp of his nature, upholding the universe by his word of power. When he had made purification for sins, he sat down at the right hand of the Majesty on high,
So the bottom line is that Jesus possessed two wills: a human will and a Divine Will. These are distinguished in Scripture but they always agreed in everything. The fact that they agree does not wipe out the fact that they are conceptually distinct. The Father, Son, and Holy Spirit are distinct, too. It doesn't follow that there are not Three Persons in the Godhead because they always agree with each other and are one in essence. They refer to each other as Subject and Object. Likewise, Jesus' two wills do not become one simply because they always agree. Nor does it imply that Jesus is two persons because He has two wills, anymore than it is implied that He is two persons because He has Two Natures (a doctrine that Dr. Craig himself accepts).