I use cardboard tokens (of each color) that depict the #6 face of the die (I basically just put the dice on a scanner and scanned them in color). As soon as the colony is placed, I remove the terraforming die from the board, and replace it with the corresponding colored token. It still takes up the spot, and looks like a 6, but can never be accidentally rolled.
I've heard alternate ways of placing a small clear plastic dome/cup over the terraformed die, again as a reminder not to gather it.
I would prefer the later over the former for one small issue:
If you return the die to the general pool, it could look like you could buy it again immediately - or missinterpret the cost for purchasing another die. With the dome, neither of those is a problem.