Yes she is a good character.
OM, I'm not so sure they are using it as a weapon. Per Pages 414 - 419:
Dresden in these pages not only reveals himself to be a sociopath (and that Protogen altered the other scientists to make them sociopathic as well) but states that their "science project" was to let the protomolecule run its program so they could understand its coding. The objective was to learn how to reprogram it and use it to reconfigure human beings to make them more "advanced" - he gives as examples being able to work in space without a suit and being able to hibernate for interstellar trips. I read it as Dresden sold Protogen on the whole sordid concept; then they sold certain covert UN departments on it.
I agree the series so far is better than the book simply because the book rambled a bit and it did get more graphic in the book. But that said, the book is still cracking good.
The purpose of the atrocity at Eros was hinted at in the series when they said that...
They wanted it to learn
Your references to pages 414-419...which chapter? My e-book does not have page numbers.