Like I said before, Deoxys is probably going to be all powerful in the movie, then at the end, they will figure out it's weakness which could be the organ on its tummy. That is probably why the PokeDex for R/S is always emphasizing that organ.
I dont think they will blow up his brain. I mean, I know it is anime and all, but it is still a kids cartoon/movie. Besides even if they did there, it would be edited here anyways....
or Rayquaza is going to have some special power not previously known of that will make Deoxys good or something. The Pokemon movies are so predictable.