Paranoid wrote:Point #2 seems fairly obvious, but #4 was the first one that occurred to me while watching the film. The whole point of their operation was to retrieve unit-01 from lunar orbit. They're very much aware that she's fully sentient, and after the operation itself they also know that she's at least partially awake (what with the laser beams). Would they risk all of their plans and have 01 possibly refuse to work, or worse - annihilate them all, simply for the satisfaction of executing Shinji?
Quite frankly, I don't think the question is "why didn't they simply kill him" but rather "why WOULD they simply kill him"? If they had faith that they could keep him from causing any more harm with the choker, then I simply see no compelling reason to.
I disagree. As far as WILLE is concerned, Unit-01 is only sentient as long as it has a pilot. Yes, they will probably expect it to go berserk if Shinji is killed
while in the entry plug based on the Fourth Angel ("Sachiel") battle, but they attribute all of Unit-01's intelligence to Shinji. For example, Asuka calls out to
Shinji when Unit-01 awakens in space.
I think WILLE sincerely believes that it is
Shinji who became a god and started Near-Third Impact, simply because they are not aware that Unit-01 has any other sentient intelligence than him. They are unaware that Yui is still somewhere inside (and probably think Unit-01 without a pilot is just a savage beast, like Unit-02's beast mode), and Ritsuko even explicitly denied believing Rei is still in there.
In fact, they might even have put the DSS choker on him, because they might have feared him turning into a Giant Naked Shinji at any time, and the device is meant to suppress exactly that (quite distinctly from its detonation button) - DSS stands for "Deification Suppression System".
However, as we should be able to deduce, it is
Yui who was Unit-01's driving intelligence during Near-Third Impact, and Yui who attained godhood, while Shinji was only concerned for Rei and blissfully unaware of any of the consequences. If Rebuild 3.0 tells us anything, the final time we see him in Rebuild 2.0 (hugging Rei on white) is also his last conscious moment before reawakening in the next movie.
I'll link you to another thread where I discuss this argument in more detail:
http://forum.evageeks.org/thread/14311/SPOILERS-Explaining-Unit-01s-awakening-in-Eva-20/