She definitely does not understand the bit where they say you have a choice. I know what they mean and so do most on here but she does not get it.
I'm not surprised that she doesn't understand what is meant and is very sensitive to external control when she's in the process of exiting a severely abusive - i.e. Controlling - situation.
Many victims of DV genuinely can't comprehend the notion of choice for a long time. DV takes away your choices and inflicts very severe suffering whenever you try to make choices. It can take years to understand and learn to make choices again after abuse.
For instance, her abuser may have presented her with two "options" but she would have known from previous "punishments" which one she had to do. Now she's got people presenting her with options outside of his system of control it's hard for her to understand how she is supposed to make decisions.
And understandable to be upset about people seemingly presenting her with choices, making a big fuss about how "it's your choice" but also making it very clear that once again only one choice is acceptable because really, does she have a choice if she wants to keep her son like any mother would? No.
Besides which, she's put herself through a lot to exit his control and now the people telling her she needs to leave him because his control is bad are also controlling her life. It is natural she is sensitive and possibly confused by that.
Rather than repeating "it's your choice", which you know she doesn't understand explain it differently. No point repeating something she doesn't understand and that is upsetting her.
"Legally it is your decision. Nobody can force you or make the decision for you. We would like you to stay in the refuge where you can be supported and then you can move into a flat in the future. But if your decision is to leave the support in the refuge now then that will raise concerns and they may take steps to xyz because abc".
If you can understand her perspective a little more it might help you to support her without getting frustrated, which won't be helping matters.