They see changes in the structure of the brain and they see changes in behavior (BPD), but they're clearly not saying that BPD caused these structural changes - they list both causal directions as some of possible hypothesis (altered amygdala/hippocampus causing BPD and/or BPD-related experiences causing these alterations in amygdala/hippocampus), in addition to other possible scenarios e.g. the fact that all of their BPD-group was on psychotropic drugs could also have been a cause for the observed changes, etc. They also aren't making any conclusions about a possible link between childhood abuse and BPD (or link between abuse and these brain changes) beyond the fact that they chose a set of 10 subjects that all had both BPD and suffered abuse; they're not even discussing a correlation as their data isn't sufficient to say anything about that.
All the observations in this paper certainly are compatible with a hypothetical scenario where these brain changes cause BPD (or indeed, are BPD) but it was some factor other than emotional trauma that caused the observed changes in their brains. I don't know if it is that way, but this particular paper also doesn't give any evidence to support or deny it.
[edit] It even seems that they don't even state that there was a change in their brains - instead, they observe a difference between BPD patients and the control group; but it would also be consistent with a hypothesis that these patients had smaller hippocampus/amygdala e.g. since birth, and simply having that property (instead of a change) was a risk factor predisposing them to suffering BPD symptoms later in life; and the authors acknowledge this as a possible option in their conclusions.
The question at hand is whether you can have thought patterns that cause structural/functional changes to happen.
> Borderline personality disorder (BPD) is a common disorder associated with emotional dysregulation and other symptoms that have been hypothesized to be related to dysfunction of limbic brain areas including hippocampus and amygdala. The purpose ofthis study was to measure hippocampal and amygdala volumes in BPD. Hippocampal and amygdala volumes were measured with magnetic resonance imaging (MRI) in 10 patients with BPD and 23 control subjects. Patients with BPD had a 21.9% smaller mean amygdala volume and a 13.1% smaller hippocampal volume, compared to controls. These findings are consistent with the hypothesis that alterations in the hippocampus and amygdala are associated with BPD.
Here they see changes in the structure of the brain.