Thomas didn’t identify Jesus as “God the Son.” To imagine that he did seems to be a desperate attempt to find the Trinity in the Bible. The fact is that it just isn’t there!
Read the context carefully:
24 Now Thomas, one of the Twelve, called the Twin, was not with them when Jesus came.
25 So the other disciples told him, “We have seen the Lord.” But he said to them, “Unless I see in his hands the mark of the nails, and place my finger into the mark of the nails, and place my hand into his side, I will never believe.”
26 Eight days later, his disciples were inside again, and Thomas was with them. Although the doors were locked, Jesus came and stood among them and said, “Peace be with you.”
27 Then he said to Thomas, “Put your finger here, and see my hands; and put out your hand, and place it in my side. Do not disbelieve, but believe.”
28 Thomas answered him, “My Lord and my God!”
29 Jesus said to him, “Have you believed because you have seen me? Blessed are those who have not seen and yet have believed.”
What was it that Thomas did not at first believe, but came to believe? It was not whether or not Jesus was God. Rather he didn’t believe that God raised Jesus from the dead. Then the risen Lord Jesus entered through closed doors and had him put his fingers into the mark of the nails, and thus he came to believe that Jesus had been raised from the dead.
Some believe that Thomas was so amazed to find Jesus alive again that he exclaimed, “My Lord and my God” in much the same way as surprised people today exclaim, “Oh my God!” when they have been surprised. Personally, I don’t see it that way. I think he was indeed exclaiming and calling Jesus his God, but in no way thinking of Him as part of a Trinity. Trinitarianism didn’t actually develop until the 4th century.
I have never denied that Jesus is divine since He was God’s only begotten Son, just as you are human since you are the offspring of a man.
Jesus is “God” in the generic sense of having been begotten by the Father (the only true God). Just as you are “man” in the same sense having been begotten by a man.
That is the sense in which it is affirmed in John 1:1 that the Logos was God. Not “the God.” That same verse affirms that he was with the God.