Its completely possible, no problem at all. The two seat backs aren't connected to each other and don't provide support for each other. Each seat back (the 60 and the 40 side) is connected at two points on the bottom where they hinge back and forth, and they each have a latch point at the top that holds them in place. I don't have any good pictures, I'm not sure if I'm explaining this well.
Basically, the two seat backs are not structurally dependant on one another. They're independently connected to the vehicle.
I did the same thing you're talking about, but removed the 40 (single seat) section and kept the 60 portion. Made an extension of my drawer system/cargo platform that extends all the way to behind the rear drivers seat, replaces the 40 seat structure, and creates some extra storage cubbies underneath.
I drove around with the seat removed for 6 months before I made the platform, just to make completely sure the remaining portion of the seat didn't loosen or something over time. Its perfectly fine. Everything's solid. In fact, my 4runner with 205K miles is ALMOST squeak and noise free, while my wife's fiat with less than 40K miles sounds like its falling apart going down the road. I think that might have more to do with how crappy her car is though