Gundato: If you had actually read the article you saw in your Kotaku RSS feed, you would see that Bungie is only partnering with Activision on a per-IP basis. Currently, they are partnering for one IP.
Delixe: You realize IW were initially partnered with Activision? It was only later that Activision bought them outright.
Again, you realize Valve has basically the same deal with EA? They are going strong.
Or are we always assuming that the worst possible outcome will occur? If that is the case, we better go warn Bungie. They might be in a talk with Activision at this very moment! I mean, you do remember that the Japanese attacked Pearl Harbor during diplomatic negotiations, right? :p
Seriously, rather than run around like chickens with our heads cut off, let's wait and see. There are some good precedents, and some bad ones. When Valve made their deal with EA, EA was still the big bad wolf.
Simply put, it is very common for larger dev teams to make partnerships on per-IP basises with publishers. It doesn't mean that publisher owns them, it just means they are willing to fund things and distribute things for a slice of the pie. And honestly, Bungie are probably going to be baking a freaky huge pie. The only thing they have ever really failed at (level design) is pretty much ignored these days anyway (seriously, compare the level design of Unreal to Gears of War), so that makes them one of the best.
Hell, isn't CD Projekt currently working on getting a publisher/distributor for The Witcher 2? :p.
Don't let yourself get fooled. Kotaku put a very buzz-worthy title on there. They spun the hell out of that article before anyone ever read it. Hell, I bet half the idiots at the Bungie forums never did. But if you DO read it, it really isn't that bad.