I think she's dead, but I can't believe they would kill her off. Carter was such an important part of the show I don't see how the show can go on without her. She is the heart and soul of the show and she always had John's back. Plus she's just so darn hot.
And thus, John falls once again into suicidal depression, starts taking stupid risks, Finch feels hella guilty but says nothing (on account of us finding out John is his....fith "assistant" and he goes throgh them like cheap socks) while getting wierdly familiar with Groves. The machine, bless 'her' tried to help but what can you do when your only voice is a ringing pay-phone? The bonds of friendship will be tested and strained to the maximum, bullets will fly in every direction untill...POOF! Another Big Bad (Simmons) to rally for and overcome, thus returning the bonds of trust and loyalty as the sun rises on a finally crime-free day.
Pure speculation, but I'm damn pi$$ed that they killed Joss. I really hope I'm wrong.
If Carter is dead (which I also hope really isn't the case), it is actually probably not the writers’ fault, as LeverageGuru mentioned. There are many "real-world" reasons it could have been "necessary", but it seems likely it wouldn't have been the writers’ first choice. I don't think they've seriously been thinking of Shaw as any kind of "replacement" for Carter, either; she brings a different element to it. It did seem true that Carter did "graduate" to a whole different level just before she died, with earning her yellow box and all, which is why I suggested maybe she'd be "dead" in the same way Finch and Reese are. She's also grown over lifetime of the show to realize that being on the "law and order" side doesn't always do what she wants it to do, just like Harold learned to use the stun gun (wonder who he got that idea from…). If this is the case, too, it might be one way to "keep" her in the sense that she could still appear from time to time in her new role, but not be so pivotal to every episode (i.e. a lighter shooting schedule if she needed/wanted that for some reason).
She's dead. There's plenty of media about it, and why.
Shaw isn't a replacement for Carter; she reflects what might be a new direction the show is going. With HR gone, they need less involvement with/by the police, and Fusco will fill the bill. What's more, Fusco still has some redemption to do. Carter was a somewhat limited character in the sense that she was a by-the-rules player (although they stretched that pretty hard at the end). Fusco, on the other hand, has a less calibrated moral compass, and has that "schlub" quality that adds a bit of humor.
But they've got to do something about the diversity in their cast.