Why is Libethenite (Cu2(OH)PO4) color green?
First of all, why do you think your copper is not oxidized? Each copper has a charge of +II while $\ce{OH^-}$ and $\ce{PO_4^3-}$ add up to -4. 

For all further discussions we need to look deeper into the crystal structure. The compound crystallizes with two crystallographically destinguishable copper ions. One forms a $\ce{[Cu(PO_4)_4(OH)_2]^12-}$ octahedron while the other one is, at least to me only fivefold coordinated to form a trigonal bipyramid $\ce{[Cu(PO_4)_4(OH)]^11-}$.
Of course those are no simple $\ce{OH}$ units as there is further bridging and connections happening but for a simple view this should be okay. So for the color there are, among other effects, still $\ce{d-d}$ transitions happening. 



EDIT:

To add something to the color change in the reaction itself. In your copper phosphate you have copper polyhedra that only feature phosphate as ligands, for the $\ce{[Cu_3(PO_4)_2]}$ these would be trigonal bipyramid and square plane.So you have the addition of $\ce{OH^-}$ to these polyhedra as well as some substitution. And introducing a different ligand will also change your splitting energy and therefore change the color.