Good question, because it's not like he needs it to be relevant in the chapter. He's saved Naruto twice already, sans natural energy. Not to mention just because natural energy is all that hurts Obito, doesn't mean Sasuke needs to be the one using it.
If Naruto makes a SM FRS and Sasuke coats it with Enton, it'll double the strength of the FRS without negating the natural energy inside it. And while Kirin isn't using natural energy, it is a natural force and thus shouldn't be canceled out by Onmyou-ton anymore than a friggin' punch or kick could.
Sasuke's fine as he is.