I actually don't see what's the big deal. It can't tell what you're doing, just at best tell the location (I wouldn't be surprised if they could only tell which reader you're closest to, not even in which direction or how far away). They're children at school where they should be at specific places anyway (or going to somewhere else with explicit permission by their teacher). Odds are they won't even bother checking to see who's where unless something serious that they need to investigate happens. Camera surveillance is a lot worse than this, and it's pretty common yet few people have a problem with that (and even less care enough to protest or sue them for having cameras).

That said, I do think that it's a waste of time and money, and RFID tags aren't secure enough when it comes to any form of personal identification.