Well kids get hurt on this at gyms across the country all the time. You don't have to believe me, but it's not my opinion. Rick McCharles has covered this extensively as well.
http://gymnasticscoaching.com/new/2007/02/the-most-dangerous-skill-in-gymnastics/
It's not like I don't have my kids learn squat ons. Obviously, there are drills and exercises. I'm glad that you seem to use these too. I don't feel "lots of kids learn it this way" if you mean one foot at a time. I consider that enough of a problem that they wouldn't be doing squat ons at all, but progressions. Still, by doing progressions such as the one in that linked video, I don't find that kids do that at all, much less lots of kids.
So, I don't agree with the way the coach is handling it, of course. As I said, it wouldn't even be an issue in my practice because if they were doing anything that could be remotely described as a shoot through, they'd be back on drills until they got it. If they're doing it like that they're almost definitely lifting their butt up into a position where a beginner is more likely to fall forward (since they'll need time and space to get their second foot on). A more piked on position is more precipitous for novices than getting into a true squat. They might be more likely to fall backwards but oh well. That's safer.