No. That would be like complaining that we don't have a license to inspect the details of and fix errors in those videos. Free software is usually not in the public domain. To be honest, it would be nice to have that option with videos (or text books!) that you get. I've worked as a teacher before -- I would definitely have exercised that option if it were available (Especially as I was teaching English as a foreign language -- I would have loved to do voice overs for some of the material I had to present). As another aside, you have no idea how much I would have loved to use assets from textbooks that we were forced to buy rather than write/draw my own from scratch -- Over 5 years, I practically had to write my own text book.
But both the point you are making and the one you are trying to refute are quite valid. By putting software in the school system, you are effectively training people to use that software. Sure, it's not software that people have to use, but it's still software that people will choose to use.
On the one hand, it's great to use Minecraft in school, because a lot of kids already play Minecraft. In this case, that's really the point. If you put in a free software project that is similar to Minecraft, it probably won't be as engaging to students.
Free software, on the other hand, opens up opportunities that you won't have with non-free alternatives. It allows people to use the software for any purpose as opposed the the purposes allowed in most educational licenses. It allows people to study and learn from the source code. It allows people to modify the code and to help their friends by sharing their modifications.
In short, both for motivated teachers and students, free software licenses are dramatically better than most academic licenses for software. I agree that you might still choose something else, but ignoring the value that a better license gives you is cutting off your nose to spite your face.
I imagine the disappointment in the face of the bright kid of the class when he asks the teacher to see how the game actually works. Still, it's better than no game at all, I guess.
It's not like Minecraft is a business tool that you're teaching to school kids, who will then go on to use it when they graduate. It's an educational tool.
This would be like complaining that Carl Sagan's Cosmos or Bill Nye the Science Guy are copyrighted videos.