I thought it was always obvious that they liked each other; that's why I knew Sakura wouldn't end up with him, which is sadly the only thing that really got me through the first arc. I hated the fact that she was still all 'Yukito-san's so cooool!', but hey, thats the way crushes go.
But Touya and Yukito were always with each other, and always either somehow touching or speaking in a way that said 'Yeah, I like you'. So...I didn't think there was controversy over that particular coupling.