I'm not saying Bungie should be ashamed of it if they did take inspiration. If they did, they definitely have their own version of it that's different enough, considering I've followed the game from the start and just noticed this. People can have similar idea's no doubt. The Matrix more than likely also took inspiration from Tron.
I guess I'm just curious as to where the Destiny story leads/ends up. Based on what's known about the lore, a similar story line to The Matrix, could be on the table. So could just about anything else though.