An organization dressed in a similar manner to the men who took Robin in the first place want to capture her alive, to me it sounds like Dragon didn't want to part with the poneglyph reader just yet.
They look more like CP agents than rebels. If you recall the first time Robin met with the rebels, she originally planned on having them take her back to Shabondy. They wanted her to stay with them, but they were willing to comply with her request.