The secret was that Arthur was king's Uther son and heir to the throne.
Explanation:
In the second scene of the drama ''The sword in the stone'', Igraine asks Merlin, “Is our secret safe. Merlin told her that the secret is safe but she is not and asked her to go to her sister in France. She said to him that all the preparations are made but asked him to protect Arthur in her absence
The secret was that Arthur was king's Uther son and heir to the throne.
The line from which Helen grey implies that the author thinks physical beauty is not the most valuable quality would be “but so you miss that modest charm; which is the surest charm of them all” there’s no focus on any physical attribute but instead on the modesty of Helen grey