I've been giving this some more thought, and I changed my mind. I don't think Kara came across as being dumb. All she said was she didn't understand the science behind the assemblers (I'm not calling it Grey Goo). I very seriously doubt Steve Jobs understands the science or coding behind the iPhone, but he's still smart enough to know that Apple needed to make it do to become the success it is.
Having Kara be someone who can see the potential behind some villains technology, even if she needs other scientists to implement it, still makes her very smart in my. So, I withdraw my agreeing that the was portrayed as dumb, and maintain my enjoyment of the book.