Possibly 2 reasons come to my mind. First, because there will be words being had behind the scenes via diplomatic channels. Any direct statement against Harry will just have him firing back, more accusations of racism, Empire 2.0, I will not be broken etc. He's a loose cannon and can't take any criticism. Best to tell the people at the heart of it to ignore him/that he doesn't represent the crown and will have no influence on policy, and to do that via diplomats, not the media.
Second, since William's statement on the Middle East is sailing close to the political wind (and has obviously been worked on and had government approval), they don't want to create a row between brothers/different rules for each type scenario in the press, which will happen if Harry gets told off (and a lot of the press is anti William having spoken).
It's classic handling of a narcissist, imo. Grey stone, don't fuel them, that's what they want.