It's like arguing that Ferrari is preventing kinds from chasing their dreams of becoming race car drivers because they charge too damn much for their cars.
plus, we're not talking about $99 to publish, we're talking about $99 just to run your own code on your own device. I don't know about you, but when I was a 10yr hacker, that would have been a deal breaker.
Is it idiotic to give iPads to school students? Yes. Is it apples fault that schools waste money on iPads? Ok, a little. But to claim that apple is the obstacle that prevents children from learning how to program wrong.
It seems that what you are asking is whether the school should take steps to ensure that kids can develop mobile applications. If that is the case then the school could just set up a single app store account as part of a mobile development course. If the school really wants people to develop mobile applications then the $99 fee is meaningless. I doubt that there is any overwhelming demand to do that on the part of students or teachers.
Of course, any kid can develop a whole plethora of applications for a variety of platforms at very low cost if they really want too. Considering that it wasn't too long ago that it took thousands of dollars to even get a computer(and many people I know didn't grow up having access to a computer of their own) your criticism is essentially looking a gift horse in the mouth. There are a lot of factors that come into play with encouraging kids to get into computers, a $99 deployment requirement for an expensive device isn't one of them.