Even with the "Oh, it's a major plot point that she gets burned" (if it even actually does happen it the book) that Benioff has been saying, there's no indication that Stannis is the one who does the burning. Shoot, in the book, they're hundreds of miles apart right now. There's no indication that Stannis is even really **alive** anymore in the Books (the Pink Letter could indeed be real, for all we know).

And, anyway, I doubt Benioff and Weiss are getting Martin's "permission" to do anything with the show. Martin has disavowed all the additional rape scenes. I do think he wouldn't necessarily have Stannis burn his own child. They've set the groundwork anyway for the North disapproving of him making sacrifices to the Red God, even in cases where it's "justified" (burning the cannibals at the stake before the Battle of Winterfell). Having him go back and burn his own daughter would be literary overkill.