It wouldn't have been right, for either of them.
He saw it in her face, the day Jack Sparrow and young Will brought her back, though they knew it would mean their deaths. He will always owe them something, for that...
But yes. He saw the despair in her eyes, when she believed her blacksmith would die, and she would have to marry him. So he let her go, and Will and Sparrow too. Better that than her hatred.
When she and Will followed Sparrow, Norrington wasn't surprised. But he was strangely happy.