I believe to change the model you would have to first import it from Homeworld into Milkshape (there is no way I have found to import Freelancer models into Milkshape). After getting the model from Homeworld into Milkshape (assuming there is a plugin), you can use Milkshape to adjust the mesh and texture. Afterwards you can use the exporters that can be found at the Lancers Reactor to export out a compatable model for freelancer.
I have not looked for a Homeworld plugin for Milkshape however. An additional program needed will be hard CMP. I suggest picking up a guide on modeling from the Lancers Reactor and using it as a guidline. The main reason for the delay on the models I am working on is getting the textures for them. There is no way I could find to extract the mesh or texture from any freelancer model.