There are plenty of airline folks with color vision issues. It's no big deal. I dont think it would cause any issues to address the fact that you were medically unable to continue in the Guard as a pilot due to a minor color vision problem. Everyone knows the military medical standards are waaaaaay above those for an FAA First Class, which is all you need for a civilian career.
The resume is a "sales" document to get you noticed as opposed to the application. You want to be crystal clear on everything on the app, along with any necessary expalantions. The resume can be more concise and focus on selling yourself.
I'm no resume or HR expert, and in your situation it may not hurt to seek the services of a resume prep expert (Kathy on one of the "other boards" is supposed to be really good), but I dont think you'll have much of an uphill battle in the civi world.
Good Luck!