I'm sure we will find out the reasoning behind her actions in episode 3. But, from what I've seen right now, I don't think it's fair to draw any conclusions just yet, because Bonnie acted hesitantly, especially when Carver started torturing and shooting people. She just wants what every survivor wants, security, which is why she follows Carver's orders. She knows she has to listen to him if she doesn't want to suffer a horrible fate by Carver's hands. This is simply her way of surviving the apocalypse in relative safety.
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I'm sure we will find out the reasoning behind her actions in episode 3. But, from what I've seen right now, I don't think it's fair to draw any conclusions just yet, because Bonnie acted hesitantly, especially when Carver started torturing and shooting people. She just wants what every survivor wants, security, which is why she follows Carver's orders. She knows she has to listen to him if she doesn't want to suffer a horrible fate by Carver's hands. This is simply her way of surviving the apocalypse in relative safety.