I encountered a study of the New Testament, in the book of Matthew where it stated that Joseph waited for Jesus to be born before getting physically intimate with Mary. Do we have scriptures supporting this or is just our faith and knowledge about God that He won’t allow such intimacy between the two while Mary is pregnant with Jesus? What about their free will? Is this asking question beyond our limitations so I sin against God?
The Bible does not specificallyl state that Joseph waited until after Jesus was born to have sex with his wife Mary. The scholar who said this is making a very reasonable guess/speculation. The Bible does not specifically say "Joseph waited to have sexual relationship with his wife until after the birth of Jesus. However, I think that most or even nearly all serious Bible students would reach this same conclusion. First of all, we know that Joseph even considered annuling the marriage with Mary when he found out she was pregnant (Matthew 1:18-19). I think we can assume that Mary was already well into her pregnancy at this time. In addition, the way Luke describes the situation, Mary was "pledged to be married to" Joseph. This means that to have intimate relations would have been adultery. It is almost inconcievable that either Joseph or Mary would have consented to sin in this way while she carried the miraculous baby inside her. In addition, Isaiah 7:15 is a prophecy that "The virgin will be with child and will give birth to a son, and will call him Immanuel." This prophecy implies that Mary was not only a virgin when Jesus was conceived, but also when he was born.
So, no, the Bible does not state in clear words that Mary was a virgin when Jesus was born, but this is a very reasonable inference from the facts we know. Perhaps the commentator you read slightly overstated his case. I do not think you need to worry yourself all that much about this issue as we simply do not know. When God does not tell us something, it is generally because we do not need to know, but I believe you can quite reasonable assume that Jesus was born of a woman who was still a virgin.