Well I would like to say its a simple 1,2,3 thing but it isn't at least at first ....
You would need to decompile the Mms.apk and then go in and manually change the color configurations. Now that can sometimes be achieved easily and other times its in more than one spot in the apk depending on incoming/outgoing messages, read/unread, etc.. you get the picture.. Each action of the Mms.apk may/does have its own set of parameters.
To accomplish all this isn't very hard if you have the proper tools and some good instruction.
1. Mms.apk
2. Decompiling tool or use APKTOOL to manually decompile it.
3. Notepad ++ or equivalent to view/modify the Android code.
4. Recompile
5. Package it back up and flash it or push it directly to the device.