Hm...
KO: I don't think this option applies to either one.
Death: Likewise. Cthulhu cannot die in a traditional sense, has spells that will make him outlast death itself, and is not some kind of flesh and blood being vulnerable to these sorts of things. Ganon is in a similar boat, where his physical form has become more just a way for his essence to interact with the world, as seen in BotW.
Incapacitation/BFR: This one could work. Hell, it's something that's worked on both before. The only problem is I have no idea if it actually would. Assuming the stars are right, then Cthulhu can supposedly travel from world to world at whim, and we already know he has trans-universal travel, so it's not like Ganon could try and seal him in the Dark Realm. Similarly, as we have no frame of reference for just how long it took Cthulhu to establish R'lyeh, we can't assume he can build some kind of non-euclidean prison around Ganon, mid-battle.
If this comes down to an actual brawl, that likely wouldn't lead anywhere, either. Cthulhu's body is just a meaningless shape he takes, and his true form is made of God knows what. Ganon has also gone well beyond the physical, but his regen takes a bit longer, unless he is willing to go into a berserk mode for more immediate access.
In short, I don't really see a consistent means of victory for either party that would either be foolproof or something the other could not escape/resist within the confines of the same battle.
