I'm colour blind too, but I have no trouble when playing PS. (I do have trouble in CS, but this is about PS so lets stick with it)
My solution: Play as TR.
As for the minimap, I don't have a problem there, but I never use it anyway apart from when I'm bombing in a lib (which is nigh on never).
And when you're using the big map just zoom into any base you're unsure of and look at the semi-transparent empire logo layered into the SOI marker.
(Maybe if all colour-blind players went to TR we'd have a fair sized pop. too?)