I don't buy that at all, jj -- firstly, most people ask "where are you from then?" at least once in normal conversation. Expecting perhaps the answer Manchester, or Leeds, or Headingley, or something. It's just small talk. I can, just about, sympathise with a teacher picking up on a kid asking "are you from Africa?" because there are 53 countries in Africa and so it's a bit of a broad question to ask. A child shouldn't be jumped on for asking it but a quiet word to the effect of trying not to jump to such conclusions seems sensible.
But any teacher who gets all riled up about the "where are you from then?" question ought to be sacked. (Possible exception: children at a villiage Primary school when the answer is, clearly, that village.)