Have you ever been betrayed by a friend, a loved one or a family member? Would perhaps the thought that if he or she had never been born your life would have been better, or at least less heartbreaking and painful? I believe the Lord was lamenting the anguish of actually being betrayed by one that he loved. He was in deep sorrow and pain. Someone else might of said; "My heart has been broken by Judas, I treated Him like a brother and he goes to my enemies to deliver me to them, I wish he had never been born."
Your question or postulation about His Word being perfect, to His purpose it is perfect, for it is not given for all to understand His Words at this (or that) time.
Luk 8:10 And he said, Unto you it is given to know the mysteries of the kingdom of God: but to others in parables; that seeing they might not see and hearing they might not understand.
Remember this earthly mission in the flesh provided our Lord with experiences and temptations that we all go through, but He never once succumbed to any temptation, always doing the will of the Father. He always acknowledged the superiority of His Father and the fact that it was the Father's will He was to follow not His own, even that the Father knows of things that the Lord does not.
Mar 13:32 But of that day and that hour knoweth no man, no, not the angels which are in heaven, neither the Son, but the Father.
Joh 14:28 Ye have heard how I said unto you, I go away, and come again unto you. If ye loved me, ye would rejoice, because I said, I go unto the Father: for my Father is greater than I.
Pax, I think I understood your question as it was meant, my apology if I am mistaken.
His Peace and Wisdom to you,
Joe