I mean, I see your perspective, but i also understand why mojang would have clauses such as these in their ToS. If they didn't, people being as clever as they are would find ways to make money off of mojang's IP.
Heck, i just looked up the wording of that section of their EULA, and I'm surprised they even allow you guys get donations.
As for copyrighting code, in their eyes there is no need to because of this passage
This doesn't give you any legal recourse like a copyright would, but at least you can get offending content removed.
and to let modders copyright could cause problems with this clause
So to me it's understandable why copyrighting, closed source and such are frowned upon by mojang. If people could do things like that, they may not be able to assimilate content that originally was a mod. Mojang would have to negotiate deals with individual modders in order to use their IP, which would be silly from a business standpoint; it is their game.
The last sentence is what I assume gives most people pause, but I don't think it should. This, combined with the above quotation basically translates to "You can copy, modify, or adapt a mod released by somebody else but may not release it"