Every single Netrunner card says "{C} Wizards of the Coast LLC." So, that's who I assume their contract is with. If you're going to argue that Wizards doesn't actually own Netrunner, or that FFG should waste time and money fighting a company whose parent company is Hasbro in court over what rights they do or don't have, just so one fan site doesn't have to get shut down...I'm sorry, you're just no longer arguing from a perspective based in reality.
There's one glaring problem with this argument: there's absolutely zero evidence to support it. You've never seen the contract that FFG has with Wizards. You don't have any communique from Wizards asking FFG to shut down NetrunnerDB. This is a scenario which you've made up out of whole cloth and apparently have accepted as fact...and yet I'm the one who's not based in reality.
Just accept that Fantasy Flight lashed out at their own fan community for reasons that were horribly misguided and stupid. They weren't forced to do it. They chose to do it. It was a dumb decision. Perhaps they realize that now, perhaps they don't. There's no reason to make up silly stories in order to feel better about what they did, though.