Still, I think practising scales has its merits. For one, it is a good drill for learning finger positions, and to fluently go from one note to another. Lately, I picked up clarinet, and I'm really finding out how important that is.
And whatever is being said about chord notes - the music is still rooted in scales. There's no understanding of the function of chords without knowing the scale they appear in. Also, it opened my eyes when I learned about the diminished scales, and when to use notes from those in an improvisation.
This way of thinking that uses the church scales to move around in a chord never worked for me, though.