There is an open source version of Orbit MFD by cjp here:
http://www.orbithangar.com/searchid.php?ID=3609
Perhaps you can play with that. If you do make changes and you want to release them, it would be worth talking about it with cjp so that we don't start having many forks floating around.
This is exactly the kind of small things that are not possible with the closed source version, and it's exactly why I like things to be open source!
There are two ways for an MFD to set its colors: set a specific color explicitly, or set one of Orbiter's default colors. It would be cool if Orbiter had many default colors, and if these could be changed by the user. Also, to avoid confusion when a user makes large changes (e.g. "yellow" to "blue"), I'd suggest using symbolic names for the default colors, e.g. "vessel orbit color" and "target orbit color" instead of "green" and "yellow".
Unfortunately, that's not the case now, and many MFDs set their own color scheme. So, for now, you'd have change colors for each MFD separately. In many cases, I think this currently involves changing the source code, and recompiling the thing.
Currently, Free Orbit MFD also sets most of its colors explicitly. Did you know that the exact shades of green and yellow used by Orbit MFD don't exist as standard color in the Orbiter API? I copied them by taking screenshots of Orbit MFD, and defining the colors from the screenshots as constants in the source code.
A nice improvement would be to read these colors at module initialization from a configuration file. If someone can send me a well-programmed patch for that, I'd be happy to apply it.