I had thought about the Guru-Guru thing as well...and as best as I can tell, "normal" time travel using the Master Sword is linear, and thus events in the past effect the future. However, it is also based on the 12 Monkeys/Back to the Future/Terminator concept that past, present and future all happen at the same time. That explains the Guru-Guru situtation. The whole game, you are traveling on the same timeline. No splits are being made. Every time you put that Master Sword back, you are teleported back in time 7 years to the same timeline. There are various theories about at what exact time you arrive, but I'm under the impression [since it specifically shows you putting the sword back] that you arrive a few minutes after you pulled it. Thus, Ganondorf is currently in the Sacred Realm preparing to make his wish. This is how time traveling occurs throughout the game.

At the end of the game, Zelda uses the Ocarina to send you back, and when you appear, it specifically shows a different cutscene than normal. Instead of the usual blue shield surrounding Link has he slowly takes his hands off the MS...Link isn't touching the MS at all. He even looks a little shocked at this. Because Zelda used a different kind of travel, and not just the Master Sword, he was sent back in a different way. Does the game specifically say this? No, but it makes sense according to some scientist's theories of time travels. He thus appears in an identical universe to his own, but at a time before he met Zelda. This is evidenced by the fact that he has no Goron Bracelet and the fact that Zelda gives the exact same facial expression in the credits as she does when you meet her near the start of the game.
Some may argue "they just got lazy and re-used the old scene", but I then ask, why did they change the scene showing Link travel back in time? Why use a new scene for one, but not the other.
I don't think Ganon ever touched the Triforce in the child timeline. He appears to be quite surprised by his ToP in the execution scene, and in the story they tell about him, they say he tried to establish dominion over the Sacred Realm...they do not say he succeeded. They make no mention of him touching the Triforce which would be a HUGE event and well noted. Also, Aonuma said that he was merely left alone by Zelda/Link until he did something outrageous. If Link really did get sent back to a time after Ganondorf entered the Sacred Realm, then Ganondorf would already have the ToP and thus, Link would not run off to chat with the Princess, or simply leave Ganondorf alone. I don't take director quotes as canon over in-game evidence, but in this case, they seem to be in unison, and that quote was part of the famous Split Timeline Confirmation...arguably the most in-depth explanation of the Zelda Timeline ever.