Actually there's an included campaign in the Draconomicon that has the PCs as agents for a well-meaning blue dragon who's in a three-way covert war with a grey dragon and a brown dragon. If you get to the very end the blue's hatchlings request the PCs act as mentors while taking over the contested territory. Which apparently involves creating a lasting bond of goodwill between the hatchlings and local villages.

It's also worth noting that there's a section that specifically mentions mule dragons- those who are born of parents of different coloration. These typically gain the appearance of one parent, and the abilities (including resistances and breath weapon) of the other. And you're encouraged to exploit this phenomenon.

Although personally I'm also fond of the Nodwick comic where the group gets hired to take on a green dragon, and manages to get ahold of an orb of green dragon control. Then they discover the entire village that hired them is red/green colorblind. The hard way.