Even though Mojang gave it the OK (reluctantly), I'm pretty sure modding Minecraft, if actually complained about, would be found illegal with the precedents we see coming out of most powerful countries in the world.
The only thing modding rests on is a gentleman's agreement.
A modder cannot own a mod, because it is a derivative work of Minecraft (one could argue that it is a seperate product supporting interoperability if the modder never read the code of Minecraft, but with the culture in North America around 'Intelectual Property' issues, I'm pretty sure that interoperability is considered infringement in the vast majority of cases. Just look what happens when somebody tries to use a legally purchased piece of hardware or software with other hardware or software the manufacturer would rather they didn't: BAM! Instant 'Piracy most foul' takedown and lawsuit.)
It would be morally wrong to use thier work without credit, but that's it.
You don't need permission to use a mod (even in a modpack!), because permission is not the modder's to give.
That privelidge rests solely with Mojang.
When making broad statements about piracy laws, one should remember that they are different in every single country.
I can only speak about the Danish laws, and in my knowledge consumer laws are thus that you actually own the copy, and have a right to resell it, or do with it as you please. This includes buying a product from a third party that works with the game.
Think of modding as a smart-phone cover: It only works when you have the original product. The mod(or cover) does nothing on it's own.
Just to be clear, you have copyright on ANYTHING you create, this include any textures you make, and any code you write.
That does not mean you get copyright on Minecraft itself, it means you get copyright on the extra content you have created, and it also means Mojang can't use any mods sourcecode without permission.
Mojang CAN however use the idea, and write their own code that does exactly the same thing.
That's the difference between a patent and copyright.