As I know, Troy is only an adaptation from the book, but it does not mean that the film should really be consistent with the book. I believe that the writer of the film has all the right to present the Trojan War in a different perspective, away from the mythical side of the book. Perhaps, he just wanted the battle to be realistic, without the deities participating and manipulating the situations. In real life, you do not see gods and goddesses taking people out of their troubles, granting them exceptional strength and determination, nor warriors fighting everyday not killing each other. The movie is probably closer to what really happened in the Trojan War.
On the whole, both book and film were only products of what we call oral tradition, a story passed on to generations after generations, a story which is likely to change. It has been so many years since the Trojan War and its story may have evolved, but the story presented in the movie Troy will always be a portion of the traditional cycle of the epic-myth Iliad.
If I were Homer, I would not care if they made a different adaptation of the story I have written, especially Troy. Besides, filmmakers nowadays would not only base their movie on a single book. Filmmakers should also source from other materials like history books.