There are rumors that Facebook is working on an HTML5 platform. Still, even if you require the use of secret keys with your online part of the game, people can still just download the source code and implement their own online version. It’s a little inconvenient, but the game itself didn’t lose any value. They just need to build their own community now – which should be easy with a great game.
I know Flash is somewhat similar, but it’s my understanding that good obfuscators can effectively make the source code so ugly that it would be a mountain of work to modify.
Native games can be cracked too of course, but that doesn’t mean they have the source code. They’ll still rely on my online part and my updates to the game.
Tell me I’m not paranoid :)