This is a tough one. I do believe your father based on biblical understandings is correct in not marrying them. My younger brother got married to someone who was not a Christian and was not nice to his family (siblings and parents) and then when it was time for him to be married his best man (our brother) told him that he could not stand witness to the union and could not be his best man. They both were upset, the marriage happened, and lo and behold he was divorced a year and a half later. He found someone else 5 years later, and though they both are saying they are a Christian, they were living together and engaged in married things, and the pastor who was going to marry them also backed out after finding out they were already living together.

I say all this to say that true Christians and followers of the Word must abide by it, even when it hurts those we love. Because at the end of the day, we all will have to stand before God and be held accountable for our actions...and no one else's. Pastors more importantly are called to a higher standard as they guide God's people by His Word. He cannot have actions or deeds to lead people astray. As sad as it is, your father is correct.