I have a theory on this whole issue. I'm not going to go into it all because we'll be here for pages reading what I have to say =P
Anyway, you mentioned how the Avada Kedavra curse was the colour green. Well I think instead of changing his eyes not to be green because of this, I think this is exactly the reason why his eyes are green. Harry, at the end of book 7, is the master of death, the true master of death as he stands up to it, he intended to sacrifice himself to Voldemort in order to save everyone else, and his bravery in the face of death made him the master of it. So as Avada Kedavra is the killing curse, and then ultimatley would be the curse of death, Harry's eyes being green I think is used to say that his eyes are almost, in a way, the colour of death, hinting at his mastery of it.
There is a better argument for that, but as I said, we'd be here for ages if I full on went into it.
Another, not so symbolic reasoning too in my opinion. I don't like it as much because it's not as fancy or 'his green eyes connote such and such'. But another reasoning that I would quite as easily accept is that his eyes are his mothers, his mother had red hair, green goes well with red and would have looked exceptionally good on her =] And so he needed to have the same colour eyes as his mother for the reasons we all know, and green eyes would have just looked stunning with her hair.
Yeah I said it wasn't as good

lol.
Kelly
x