I doubt Bio is unhappy with EA. But EA let go of Pandemic Brisbane a month ago because they failed to release that Batman game. I mean wow. Set into the wild. Not shut down. Just let go. That's great if you ask me.
Yes, yes, they're a division, blabla. But it's still the same company, and still the same people there working. It's not like they fired all Bio staff overnight, replaced them with EA staff and only keep the logo. That's just ridicilous.
Besides, the Bio doctors are also EA vice presidents, so that means they have some say as well - OVER BIOWARE. And yes, they keep doing what they want, after all, that's what makes Bioware so succesful. They make the right decisions that benefits them (creatively) and EA (economically).
BIS is a flawed comparision, as BIS was created from Interplay, and only existed as the RPG label. But Bio was formed independently. Bio is Bio. EA would be stupid to change that, and everybody knows that.