Ah many thanks Trickstick! Exactly the kind of reasoning I needed, and I am not an expert on the fluff.
BTW, this is for
AT/SM1. I got a brand new Space Marine v1 game, and while deciding on how to paint the minis, I decided to pick out 4 legions from the sides of the box and paint them up that way, even if they arent canon anymore. So with 16 Land Raiders, 32 Rhinos, and 64 stands of infantry, I decided to divide by 8 and make 4 Loyalists vs 4 Traitors. I've gotten a lot of other bitz, and want to distribute them evenly between the two, but make each unique amongst the sides!
Pics are at the bottom here;
http://thefallenprinces.blogspot.com/2012/08/epic-space-marine-lots-of-pics.html
So rather than painting one half all Ultramarines, and the other Sons of Horus, I thought it would add a lot more character to do it this way.