Nah, the rest of the good guys would be there. And we would be seeing expel showing up en mass. The entire human population aside from SEELE would be untanged within a few weeks. And that's simply because there's only so much shoreline that people can return on.
I don't think they need much in the form of restraints. Also all that's missing is someone telling them how badly those things itch.
Don't worry, Gendo is going to get WAY worse.
I would have her dating one of the bridge crew, namely Makoto. Kyoko's dating Shiguru.
And all the surviving NERV staff.
Oh he doesn't need to do that. I mean, Gendo changed his last name to Ikari, which is Yui's last name.
That's to be expected.
Ohh, they would probably do some checks and then sign them off as "unwitting/unknowing pawns".
They won't, but they would be lacking any support from the JSSDF. Which was probably unwilling anyway (You Are (NOT) At Fault had that as they're reason for attacking, basically either they followed orders from one guy who was actually part of SEELE, or they and their families are shot dead).
If he didn't decide "Fine! I'll do it myself", gets his own custom Eva (similar to the Black Ace in Going Another Way, which was controlled via his cybernetics instead of the usual methods), and then shows up as the "final boss". And at the end gets either completely vaporized, or is tanged by Rei and Kaworu, giving him the immortality he desired, but not the way he wanted it.
Or taken out as the "final boss" if you will.
