How about instead of Link jumping from one time to another, time instantly fastforwards, or rewinds.
Example. Link pulls out the Master Sword. He goes into the Sacred Realm, times goes by really super fast, he comes back into Hyrule as if it was instantaneous, and vice-versa.
So with this in mind, when swapping between the two times, every action that has occured is either repeated, or undone, depending on which direction one is travelling.
With this also in mind, let's remember that Ganon was sealed away inside the Sacred Realm, however he was inside a
void that was inside the Sacred Realm. Now this is the part where this theory relies on assumptions; the assumption that this void in which Ganon is sealed is outside of time. Therefore Ganon, being inside the void, is not affected by things that happen in either Hyrule or the Sacred Realm, because he is sealed away from both. Thus, if Ganon becomes sealed inside the void, then time is turned backwards, it does not affect Ganon. He remains inside the void, whilst everyone else is taken backwards, their actions being undone as time turns backwards. Everything that has happened because of Ganon's actions is undone because they are still in either Hyrule or SR and are subject to time.
So to sum up: if Zelda sends Link back, everything gets undone up to the moment that time stops turning backwards. Ganon is outside of time, having been sealed inside the void, and everything he does gets undone, but he does not return to the past, therefore the future he created cannot happen, and as far as the people of that time would know, he just disappeared in thin air. That way, Link can go off and do his Majora's Mask stuff, and the tale we hear about in TWW can follow through. Diagram included for any confusions in my explanation:
I dunno what all of you consider to be the correct timeline or whatever, but I'm not about to debate that. All I'm saying is that if Ganon's void is outside of time, and time gets turned back, then he disappears, and everything he did is undone.
You don't have to agree, hell, it doesn't even have to make sense to you, but this theory helps me wrap my head around the whole time travel concept and the resulting paradoxes. Makes sense to me, so I'm sticking to it myself.