That dummy system is going to f*** some s*** up. Maybe Shinji could have found a way to defeat the Eva without hurting Toji. But now...well..... everyone whose seen the anime knows what's coming next.
Even though its pretty apparent that this whole situation is one botched up plot device to push Shinji into the depths of depression, I've always wondered if he could've used his knife to cut those web things from the Angel that were around the LCL plug. Then Toji could've just ejected from the Eva....
Instead of nowt wanting to kill a fellow person like in the anime anime, Shinji doesn't want to kill his friend Toji. A very different nuance, I think. That's the only difference in this chapter.
I liked how Shinji stuck to his guns and refused to endanger his friend, but I know I would have made the exact same call that Gendo did and initiate the dummy system.