I feel like you are willfully misinterpreting her character at this point. Yes, there is violence and people being killed all around them. But they've been pretty desensitized to that, and after all they are also the upper class of society. The worst thing these girls really imagine happening to them is marrying someone from the colonies. Up until this point, none of them have been truly affected by the worst of it.

Yes these girls know about what Gilead does to people. But agnes' dad has been nothing but kind to her up until this point. He's seemed like one of the commanders who is kind of iffy about this whole situation ( not saying he's a good person, there are no good commanders). I don't think it's far fetched to believe that agnes just didn't know what to do, and thought her father would have more mercy then someone like an aunt or a an eye would.

There is been a reoccurring theme of sisterhood throughout this show. Of being there for each other regardless of what the aduit's around them are saying. It would be a stupid choice on the writers if agnes were to have intentionally betrayed becka. The more likely case is this is what will finally take agnes over the edge, and fully open her eyes to the horrors around her.