Sure, if you're a big enough Metroid fan to be buying Trilogy despite already owning the game, it's likely you already have Metroid, either on the NES, the Virtual Console, or as a connection bonus on the GameCube Metroid Prime disc. But it's still wonderful precedent to have Nintendo giving away a Virtual Console game to promote a new release.
But why limit it only to the suckers buying one of the games twice? And why only 5,000? A Virtual Console download costs Nintendo nothing.