I wouldn't count Holly out quite yet. They've set Beverly up as ripe for "redemption." She's becoming aware that the evil she's been fighting isn't the people in the Eureka trenches (Carter, Blake, Stark, etc.). It's the "military industrial complex" that she's become a part of. But now, she finds herself on the outside. She's the unexpected voice of morality who starts to see that the "cure" for Eureka (the Consortium) is far worse than the disease. As a misguided idealist (like her father Adam), she may turn on the Consortium, and the first act of her personal salvation might be to "resurrect" Holly and work to deliver Eureka from the hands of Senator Win and her evil cabal.
Just a theory.