Many middle schools/high schools in my area teach computer science (programming mostly) with Minecraft. Its a good starting place for showing kids in a familiar environment what they can do with programming.
Is it, though? Admittedly it's been a while but I feel like once you get beyond the absolute basics of circuitry Minecraft gets ridiculously complicated in terms of building the structures necessary to establish the circuitry (just search YouTube for the monstrosities that are necessary to build simple adders in Minecraft). At that point you're not really learning anything except how to play Minecraft.
When a student's at middle or high school level I feel like LEGO Mindstorms or even Arduinos would be a better option.
It's much like the arguments that often come up here on HN where the flavor-of-the-week framework or language is being inefficiently twisted to fit a purpose it wasn't designed for.
Similarly, children are already playing with Minecraft and are interested in doing "cool stuff" with it. If you can tap into that existing goal and use it as a way for them to learn something else, it's less of an uphill struggle since they'll be intrinsically motivated to learn.
[1] http://services.minecraftedu.com/wiki/Teaching_with_Computer...
For your specific redstone logic problems, try the "project red" mod. Its in plenty of FTB packs.
http://ftbwiki.org/Project_Red
You could make some points about chemistry using minechem. Maybe not much deep knowledge but something basic might seep in.
Across many mods there tends to be an inherent bias toward industrialization / capitalist investment. Produce things slowly by hand or quickly with an assembly line and even faster with speed upgrades.
I suppose there are kids who are extremely fuzzy on the basic concepts of steam based electrical power generation and railcraft and big reactors would clarify some of that.
There are probably ecological lessons in terrafirmacraft and the numerous food mods. Not all of minecraft is "apples come from oak trees" or whatever.
I suspect it works very well for shallow gaining interest, very well for signalling, not so well for serious learning. Kinda like ipads in schools. Or computers in school, in general.
True...many students do stop there...but others may be inclined to follow up based on interest, or curiosity...children's minds veer off in unpredictable ways, just as adult's minds do...exposure to new concepts is ultimately what education is all about...
I think your question is valid...I'd love to see what would happen if a class of 8th graders were given a Raspberry Pi at the beginning of a semester and asked,"What can we do with this? Then give them the whole semester to answer...