No real surprise considering Mario Galaxy's composer, Mahito Yokota had to repeatably beg Miyamoto in order to get one. Looks like the future of orchestrated music appearing in a Zelda game lies in Aonuma's ability to beg Miyamoto enough to get it.
Of course I wonder if maybe someone like Miyamoto might consider allowing the Mario Galaxy games to have an orchestra a lose on his part and so as a result he's going to refuse allowing Skyward Sword to have one no matter how many times anyone begs in order to feel like he's in control again. You can never tell with Miyamoto since some things make him seem like a really nice guy who's fun to be around while others make him sound like an ego driven maniac who needs everything to be done his way or the highway.
Actually, that's wrong. Mahito Yokota wanted to use Latin & synthesizer music for Mario Galaxy, while Koji Kondo wanted to use orchestral music, and when presented with samples from both, Miyamoto chose the orchestral piece. In fact, for Mario Galaxy 2, the composers were unsure about putting together an orchestra again, but it was Miyamoto who stated it was necessary and green-lighted the orchestra immediately.
I don't think he is opposed to orchestral soundtracks - he probably has his own idea about when it's appropriate. With regard to Skyward Sword, I reckon it is perhaps more appropriate there than any other game. Does Miyamoto feel the same? Who knows? It isn't really worth reading too much into that quote though; it doesn't say that much for or against the idea.