If some people's hypotheses are correct and this is a remake of zelda 1/2 or it's in the same timeline branch, ganondorf will have permanently become ganon (due to touching the triforce and having his desires come to fruition) so you'd have no choice but to fight pig/board ganon. Unless he somehow gained control over his human self again after being killed in Zelda 1. In zelda 2 you delayed his resurrection by getting the triforce of courage, but he can never be killed permanently.
Never heard of this hypotheses, seems interesting. What are the clues that support it?