Thanks for your comments! Some thoughts below.
Yes, everything that you say is true, or at least conventional wisdom. And, I'll probably end up on that path on the way to teaching Physical Computing. After all, what would a course on programming a microcontroller be without ending up in C, and the Arduino IDE does that well.
But I think one might take you to be dismissing a huge swath of unexplored territory with your statement that "If the arduino is to be used only in a PC connected environment ... then I can understand using Calico or Processing or whatever." There are two ideas here:
The first is that using Calico allows many different languages to connect to the Arduino. For example, by following along the blog, one could also program in Calico Jigsaw (a visual programming language), or Calico Scheme (a high-level functional language). More importantly, each of those languages opens up different audiences to the Arduino. On one end, Jigsaw might allow even younger than 4th graders to get some experience with embedded systems and computing. On the other, Scheme allows some possibly very interesting high-level code to be explored. And there are more languages in Calico that get this connection without additional work.
Second, there are many possible projects that exist before jumping to embedded only (many ideas that can be explored in Processing or whatever, too.) But before we completely move to C, let's play around a little to see what is possible in combining the power of the PC with the embedded system. I don't mind spending a little time in this space to play around.
So, in true DIY maker spirit, we're just hacking into unexplored territory.