Terra's hair was green because of palette limitations. Celes uses a different palette that has the yellow color in it, so her hair is blonde. Terra's particular palette, which she shares with several different characters, does not have the yellow color in it, and so the programmers were forced to use the next best available color, which was green. These kinds of space limitations commonly affected how characters were portrayed back in the gold old days of gaming.

And Garnet and Eiko do have blonde hair in their trance modes, so Amano's art wasn't completely disregarded. The thing is, though, Amano likes blondes. Alot. Almost every woman he's ever drawn is blonde. If FF was solely up to Amano, we'd have almost nothing but blonde-haired characters.