How about extreme time distortion from warp travel? Say you are in command of a legion strike vessel (let's say Iron Warriors) with a small contigent of legionaries. you have just won a great victory on Istvaan V. You get orders to conquer some backwater world to use as a suply dump. You head into the warp- and when you come out the chronometer reads M40.581 and when you make planetfall you find the people worshiping the Emperor. And it has nothing to do with Lorgar- they have been worshiping the emperor for 10.000 years now. And on the frescoes of the imperial basilica you find a mural of the emperor slaying the beast Horus. Now what would you do?
Bear in mind: you have NO idea what happened after the drop site massacres. Maybe you have seen the eye of terror on a galactic map, but you have no idea thats where the traitors fled to. You might be able to find out from the populace that the astartes are the emperors angels of vengeance. What do you do? Head for Terra to fight for a warmaster that is 10.000 years dead. Or is it more likely that you pretend to be some obscure space marine chapter?
Unless you somehow can make contact with traitor marines- and even if you can, do you still want to join them once you see what they have become? (especially the deathguard!)
Well, if you had turned traitor, you'll more than likely remain so, and probably head out to a Warp tear to regroup with the rest of your kin or become a band of raiders. Finding out that traitor marines fled to the warp is not too difficult, but getting there, and getting in without getting destroyed by the warp and hordes of other heretics and traitors might be a bit more difficult. Becoming raiders is even easier, since you already have a ship and serious equipment; you just have to find more up to date navigation charts, and are set for the most part.
However, you might reconsider your past actions based on the consequences they had (most of you fellow have become chaos tainted abobinations, which you never signed up for), and become some form of renegade chapter ala Soul Drinkers, still affiliated with humanity if not the Imperium, and operating outside the standard command structure.
More interestingly, if you get warped to the modern era before your legion turned traitor, you have an even greater dilemma; all you knew about your legion has changed, but if you can find out what truly happened during the Horus Heresy, you may find that the Emperor is not without his own sins. In any case, you'll have to chose between rejoining the ranks of the Imperium or turning your back on it, and, either way, you'll probably want to change your name and heraldry for something not directly associated with the most famous traitor chapters in history. If you change your heraldry, or have one that is not immediately recognizable as traitorous (like the pre-heresy World Eaters, Thousand Sons or Luna Wolves), you should be able to escape any serious scrutiny, and integrate back into modern society as just another chapter long lost in the Warp without too many issues after a getting acquainted with the historical events of the last 10000 years and current state of the Imperium.
This has actually been done (unofficially). The time displacement, choosing what to do with yourselves, it's the story of the Knights Repentant, a /tg homebrew chapter made up of pre-heresy Word Bearers. Oh, what was that page again?
http://1d4chan.org/wiki/Knights_Repentant
There we go. I highly recommend reading the fluff parts, it's good stuff. Here's my favorite part:
"They searched all of the records, all f the archives and all of the libraries searching, desperately searching for something, anything. Something to make the nightmares they now saw when they closed their eyes and imagined the future that never was, something that could prove all they had witnessed was a bad dream, something to reveal a diabolical ruse. They found nothing of the sort. But they did find some things. They now had a rudimentary knowledge of this new and terrible era. They knew what awaited them.
The only logical thing, the Adeptus Mechanicus claimed, was to run. Flee to the horizon and never, ever stop. This dreaded Inquisition would find them. They would be hunted, and if they did not break orbit immediately they would be put down like rabid, mongrel dogs.
But they had faith. If they were to die then they would die as men, with dignity, not fleeing like rats from a fire. Weapon systems were powered down, shields were lowered, engines cooled, and all over the fleet, the hymns of sorrow were sung. It was a cold and lonely night as they waited for judgement."