Hmmm.... Perhaps he was turned to stone because it was a repeat of events? In the first flood, Hyrule was sealed away. Everything was frozen in time- grayscaled. Stone is gray, and while being frozen and being stone are different, they are both stuck or "sealed" that way. So, perhaps Ganon's being turned to stone (similar to the greyscale) was done in order to show that his fate was "sealed". But that's only looking at it from a symbolic point of view.
We do know that he is indeed stone and not grayscale, because he is stuck in one shade of gray and we hear that rocky noise that is often used in similar scenes in other forms of media. It seems, though, that Ganon had become the pedestal for the Master Sword. That scene screamed Sword in the Stone. And, in other games, the Master Sword has to be pulled from its pedestal. It is possible that Ganon is so powerful that the Master Sword is acting as the key to the seal. Ganon was a wizard of sorts, even before obtaining the ToP, so even without it, he's still a threat.
I do think that you are right in suggesting that it is because it will be used in a later game. More than likely they are setting it up so that an evil villain will wreak havoc and the Master Sword will be needed to defeat them, but pulling the sword from its resting place will only bring about more trouble- the freeing of Ganon. Or something similar to that.