AFnord: If the EA "indie" bundle did not contain indie games, then a lot of other "indie" games (like Bastion, LIMBO and so on) are not indie either, as they were published and at least partially funded by larger non-independent publishers. EA published and helped fund the games in the EA indie bundle, but the companies behind those games are still independent.
This. In my opinion those are still indie games despite being published by a bigger company. Otherwise there are many games on XBLA and PSN that you certainly wouldn't be able to call indie (like Journey) just because they are published by either Microsoft or Sony. Anyway, there is no clear of definition of what "indie" stands for.
Klei, the indie studio that made Shank is still independent, and i think that this is what matters. Their lastest game Mark of the Ninja, for example, was published by Microsoft, not EA. They don't belong to any company, so they pretty much have creativity control over their games.
For me there's nothing wrong with big companies publishing indie games. I guess some people just want to find irrational reasons to jump on the EA hate bandwaggon.