With HRH wishes & when it is time to take the place of his mother (may it be not, for many years to come) I would hope that 'Defender of the Faith' is kept in accordance with tradition, but, have something like 'Keeper of all faiths' included so as to recognise the vast display of religions practiced by many of his subjects throughout the world.
eg: "By the Grace of God, of the United Kingdom of Great Britain and Northern Ireland and of His other Realms and Territories King, Head of the Commonwealth, Defender of the Faith, Keeper of all Faiths."
This is of course one of many options that can be pursued.The above addition is purely and utterly my own take on the matter & it doesn't have to be 'Keeper'. It shall be whatever they feel appropriate I am most sure. Thats if they feel it appropriate at all...time shall tell.
"MII"