John\'s intent was to wed Mercy but, much to his suprise and shock, Judith misinterpreted his words.
To answer your question I will quote directly from the text:
\"Then, still incredulous, he looked back at Judith. Every trace of pride and haughtiness was wiped from her face. Such utter happiness and trust shone from those blue eyes that John faltered, and in that moment of hesitation he was lost.\"
As an aspiring clergyman, John could not intentionally hurt Judith. He chose to set aside his own feelings to protect hers.