From what I can remember and then speculate on, it seems like Kefka was in charge of the MagiTek soldiers part of things. Cid oversaw the extraction of magic and the imbuing of them with powers, but Kefka made them into soldiers. I guess, in that case, Terra would have only had Kefka as an authority figure and so I guess I can see why she was a little smurfed up.