You can change beam/laser/whatever colors by changing the texture itself with Photoshop or another editor. Tried changing them in the weapons section but that did not work
Axel, for beams there is a section in the weapons section that explicitly defines beam color, and this does work**. Most other weapons you're right, you'll need to edit the textures.
** It maybe possible some beams have their color predefined in the texture. When I changed a Vasari pulse beam's color to purple, it worked but the pulse beams seem to have a second beam after effect which was still green. I didn't check because I thought it was cool how it turned out, but its possible the main beam was in greyscale, and was thus recolorized with the info from the beam weapon, while the after particle's texture was explicitly colored green.