how come the crystals which come with the sabers from the war hero vendors only seem to be green for the republic? i assume its red for the imperials?

The ones which are in the PVP weapons are chosen to be suitable colors for your faction.

 

If you want a differently colored expertise crystal, you can either craft one if you have the schematic and Artifice crafting skill, or you can buy one off GTN, or you can buy one off the PVP vendor, or if you have access to the pre-order crystal vendor you can buy one from there.

FYI

Here is a list of all the end game crystals with pictures as well as where to obtain them.

http://dulfy.net/2012/05/07/endgame-color-crystals-post-1-2-and-how-to-obtain-them/