I think the idea has a lot of strength for the story, it really reinforces the idea that Gannon is doing good things for Link, truly taking him under his wing and helping him become a thief, which adds to the ambiguous undertones of the whole story. It also makes the most sense, since the whole thing, Gannon teaching Link to become a thief, is what's driving the plot.
Miles has some good points though. This would make it impossible for Link to learn the techniques after the point in the game when you have a showdown on the balcony and Link's gang, Zelda, and Faron confront you to expose Gannon for being the evil king he is. So since there's still a dungeon after that and you can presumably still explore the world, this would make some areas permanently inaccessible/some sword moves permanently unlearnable if you didn't learn the technique before Gannon's true identity is revealed. Which is kind of crappy for the player.
The way you CAN make Gannon Link's sword/thief technique teacher without the possibility of robbing the player of techniques she/he forgot to learn is to make every one mandatory to learn and teach them all before Gannon's unveiling. Which takes away the excitement I think is great about optional/bonus/secret sword/thief techniques.
So my inclination is to say maybe Gannon would be able to teach the thief techniques and make them mandatory, but have the sword techniques be from someone else, or else have Gannon teach you one or two or three things that you have to know before the end of the game, and the rest you learn from someone else. But you know, it's a good idea so we should make it work if we can. It'd definitely avoid gameplay problems if someone else was the teacher, but it'd be less impact flu to the story.
I'm a little confused about the alternate ending thing too. I think the plot has always been that Gannon was using you to steal the cogs for him, and was always going to "betray" you, as in he would be revealed as evil. What would cause an alternate ending/what would change?