if you don't know about using the modtools start here, and check oheckout the mini tut on editing sides.
index.php?name=PNphpBB2&file=viewtopic& ... f&start=15
if you know how to use mod tools a quick and dirty way would just be to edit the alliance "side". youd have to do a little more than dead said i think because you would also need to rename all the weapons.
you could edit the alliance soldier odfs and add/edit/subtract the attributes the alliance troops had like the actual model, weapons, abilities. IF you know how to use the modtools i think it would be pretty easy, i think. Just start out by trying to swith models:
edit all_inf_soldier.odf
GeometryName = "all_inf_soldier.msh"
GeometryName = "all_inf_soldier"
AnimationName = "all_inf_snowtrooper"
GeometryLowRes = "all_inf_soldier_low1"
with the following taken from rep_inf_clone_trooper.odf
GeometryName = "rep_inf_trooper.msh"
GeometryName = "rep_inf_trooper"
GeometryLowRes = "rep_inf_trooper_low1"
AnimationName = "all_inf_snowtrooper"
now copy rep_inf_trooper.msh and rep_inf_trooper.tga from C:\BFBuilder\Assets\Sides\REP\MSH to your mods \side\REP\MESH folder,
munge and test. if that works you can use the same method to bring over weapons and stuff
Anyway i think that should work unless i missed something(very possible).
just remember that if you make a reference to another odf/mesh/tga/...
that you have to have that in your sides folders, so be careful of weapons becuase they might call another odf for ord, or tga or whatever.