I think the protruding camera is a necessity at this stage.
To create a good camera, you need that thickness, reducing that dimension is the worst thing you can do to a camera team.
I think if Steve Jobs were still around, hed explain it like he explained the sun flower Mac design.
Everyone was expected a thinner iMac. We not had flat screen displays, so it would make sense to create a flat screen iMac, with the computer enclosed behind the screen, but the technology wasnt there to make it work well enough.
Hard drives and Disk Drives at the time only ran at their fastest when they were horizontal, and if you attached all that stuff to the back of screen it would no longer be flat. Good design is a result of functionality, so Apple decided to let each component be true to itself. If the drives wanted to be flat, let them be flat, if the screen wanted to be flat, let it be.
Same here, the camera, to be the best it can be, needs to be thicker than the casing of the phone. Apple could do two things here, make the phone thicker, and have the camera flush with the case, or have a protruding camera. This means the phone is as thin and light as it can be (Something Apple values) and feel great in the hand. The concession of having a protruding lens allows the phone casing to be its optimum form, while at the same time, allowing the camera to be as good as it can be.
If they went for a flush design, either the camera would be crippled, or the form of the phone would be crippled.
Now, personally, Id like the phone to be a bit thicker, and allow for a bigger battery, but Apple have obviously made the decision that size and weight are their key goals.