Saying the door of time is closed and no one else can use the MS are 2 very different things. Also note that we know the MS is used by other people after OoT so there goes that theory. It's pretty clear that she's saying timetravel will no longer be possible for Link, and that if he wants to be young again, she can send him back.
Zelda mentions, that, by returning the Master Sword and closing the Door of Time he will close the paths between time, but I think she meant with that that no one eslse could open it nor use the Master Sword. I also think that Link could have returned much time later to the future according to my theory, since he practically had 7 years to do it until he woke in the future.
Aside from the fact that Zelda has already told us that the MS cannot be used to travel time already, it's extremely anti-intuitive that Link would go forwards years after being sent back to being a kid by Zelda. There would be no point in doing so, and it would make the ending of sending him back to regain lost time redundant.
But then, if you believe time travel to work that way, how can you solve the paradoxes that it implies?
My theory is that time is linked when Link travels during OoT, and it is only after time has been set in stone that Links traveling to the past has an effect on the 'universes'.
If you consider that time can split at one point of time travel. Then why shouldn't there be splits everytime a time travel occurs? In my split theory, I believed there were multiple futures where Ganon reigned for 7 years, and multiple timelines where Link prevented the 7 year rule. In essence they each have the same premise, so there's no need to focus on all of them.