I used the word "material", implying samples, not complete organisms. In order to study organisms, bioengineer them, and clone them, you need actual raw material to work with, along with any useful work that's been done before you. And all those samples are scientific treasures, precious stuff. Seele wouldn't be able to just order them all destroyed as soon as the harpies get sent out, either, since they don't know for a fact that they're going to succeed.
So if you went to any one of the labs Seele had been funding, you'd probably find everything necessary to generate a "god" (or god-stick), provided the technology could be brought back online. You might even find one of the Evas or Spears that didn't get finished in time.
Fair enough, but I have my doubts that a substantial amount of that stuff survived Third Impact and the chaotic aftermath. I wouldn't assume there's any stuff left, and the obvious intent of the scene, imo, is that nothing remains to build a god, even if they fucked up in that presentation.
I do not believe that she went through the CI with shogoki for Shinji's sake despite what she says in the few scenes we see her. We are talking about somebody with a direct - dare I say intimate - SEELE relationship and with a deep understanding of all the scenarios involved. You do not "help your son" by making the worst scenario come true (instrumentality successful) under any circumstance, or relay your choices to him exculpating yourself in the process (after all, you know that the traumatic experience of losing you and being left with the emotionally unstable and immature Gendo will turn Shinji into the usual, highly degenerate, indifferent and worthless self - tormented pawn he ends up being).
It was either that, or be assassinated and have absolutely no hope for Shinji's future. She has a bleak option and a hopeless option; there's no third option she could've taken that would've saved the world without crushing Shinji's fragile little soul.
(4) Tried and true trope is tried and true.
TV Tropes link? In MY Reichu-post? Oh ho ho.