I have no idea where this comes from but as far as I can see the statement that Link dies because of Ganondorfs spell in OoT is just speculation! In the Book and the translation of it on Zelda-Wiki it just states that "The Hero of Time is defeated". Now to defeat something or someone is a very broad thing to say. In my opinion it is the following way:
When Link goes 7 years through time for the first time he stays on the original timeline, where Ganondorf puts Hyrule into Chaos. Now in the future he does some things that will help him in the past. Then he actually goes back to the past were he is still on the original timeline. In the past he has abilities and things that help him change this past and because of that he afterwards went to a different future, thus abandoning the original timeline for all eternity, because he created an alternative version of it. So in the original timeline Ganondorf will take over and conquer Hyrule and that leads to the Sealing War and ALttP. That was the defeat of the Hero of Time, simply because he had to change the past because he wasn`t strong enough to fight Ganon(dorf) in that future...
Now in the alternated future he is strong enough to defeat Ganon and Zelda sends him back to the past. This is the timeline were there is no Link, because he was send back, and therefore the goddesses had to flood Hyrule which leads to WW.
As I said Zelda sends Link into the past in which he warns her young self and that's why Ganon gets executed (and eventually at some point sealed away, since tha's what his state is in TP), which leads to MM and TP.
I know it is complicated but I don't think that people should think defeat=death. But it actually makes a lot of sense!
Also there a still many holes in the overall timeline, like between MM and TP and on some other parts of the timeline so hopefully we`ll get these awesome games some more years
