PreTty much what CP said. I feel Terra was given green hair to distinguish her from Celes, but also due to her origins, its just a visual reminder of her otherworldy self. I'll admit it works, cause watching the CGI sequences in Anthology, it can be difficult to discern which is Terra and which is Celes by going on their faces alone.

In a way, I felt they did it for the same reason why Faris and Leena have pink hair in V, cause if they made them blonde like, Krile, it would be visually jarring for the player.

Personally, I'm more curious as to why Garnet and Eiko are not blondes like their Amano artwork, (besides the fact Amano just has an obsession with that hair color for females) seeing how FFIX easily had the technology to do so and there is no in-story reason to give them alternate hair color.