EA still has the rights to the classic C&Cs

However, If I remember correctly, they can only shut down projects like this if it directly affects their profit or profits from their intellectual property.
In this case, EA would have to make at least a portable C&C game to have a case, and probably a DS C&C to have a good case.
Besides which, EA has a (somewhat unofficial*) policy not to interfere with nonprofit stuff based on their games.
*Confirmed by Aaron Kaufman, but I'm not sure about their corporate policy specifically