That shouldn't be a problem for a bodyshop to do. I'm actually in the same situation. I'm planning on getting a CF hood for my car in the future too. In fact I was thinking that I might get a clear coat over the CF with a blue tint. I don't know, is that r*cey?
If you look into the newest issue of Import Racer magazine, they show how they had their CF WRX hood done up with a clear coat with a blue tint. Clear so you can see the CF weaving but with a blue tint.
They basically mix a bunch of clear coat together with a little bit of blue to match the car, then they paint the hood.