Master of Orion ]I[ has been modded by the community to be much better than it was upon release.
As for legal issues... Theoretically, they are using LA's own files in the game to restore content whilst adding their own (presumably), the downloads aren't for sale, they're not using the content to make or mod another game, so I don't see any copyright infringement.
IANAL, but I handle software permission contracts at my job, so some knowledge of copyright law is kinda required.