Demonhunter: You may not realize this, but not all of the OoT carts for the N64 had Gannon with red blood. The first batch had the red blood, but somewhere down the line Nintendo caught flack for including it, so they changed it to green. So, if you bought the N64 OoT at a later date, you may have gotten a version with green blood. So, this is not just a new development for the GC version.
Frankly, I was surprised that the ESRB let the red blood go in the first place (or maybe nobody at the ESRB actually played the game all the way through while they were reviewing it, wouldn't surprise me). I'm sure some uptight parents/watchdog groups howled and complained, and rather than have Zelda slapped with a Teen rating for such a stupid thing, Nintendo just decided to change the color of the blood.