As a jazz educator, I can see why there is cause for concern; if you give everyone the same tunes to learn, the same solos to transcribe, the same scales, etc....then yes; theoretically, you would have legions of musicians who sounded the same. The good news is that this is a theory. In reality, most musicians, at least in jazz, end up sounding different eventually. This is because jazz music encourages originality at it's core. Even the most conservative program will produce students who don't sound identical.
I think that this idea of "not wanting to churn out a bunch of musical clones" is at first glance, very logical. However, in the long run, I think it's actually worse to "churn out a bunch of musicians who cannot play well enough to work as musicians in the real world." I'm finding that my own misgivings about teaching in a "cookie-cutter" fashion are being overrun by worries about not producing students who have the necessary skills to be successful.