You can change those colors in the prefs.ini file, which is located in My Documents\My Games\GalCiv2
The relevant lines are here:
[ForeignTreatiesWnd]
LineColorAlliance=-16735745
LineColorWar=-65536
LineColorTrade=-2778349
LineColorTeam=-16711936
The colors are in D3DCOLOR_RGB format. Open up a paint program that allows you to mix your own colors and find the values of R, G, and B that create a color that you can easily distinguish. R, G, and B are integers between (inclusive) 0 and 255. Then get out your calculator. 
This is the formula for creating a RGB number:
(255 * (2 ^ 24) ) + (R * (2 ^ 16)) + (G * (2 ^ 8)) + B
Also, in case the 2 ^ 24 notation isn't clear, that means 2 to the power of 24.
You can also change the tech category colors and the TradeWnd's accept/reject colors in the Prefs.ini file. When I get the mods folder working, you'll be able to even change the various race colors.