Sorry for the wall of text, but this is a radical idea inspired by the awesome ideas of bringing the characters to coruscant in ROTJ and I thought a lot about it early this morning. Maybe i'm crazy, but I wanted to see what you guys thought.
How about inserting a scene/sequence in ROTJ or earlier in the series at some point which explains that the fate of the clone/storm troopers is tied directly to the Emperor's life? IE, it's bred into them just like order 66?
That may seem crazy/illogical and awfully convenient for our characters.....but really think about it. Does it not fit perfectly with Palpatine's character? Remember, he is meant to be the ultimate embodiment of avarice, and he is distrustful of EVERYONE. Tying his own fate to the clones insures that there is no plot against him in the power structure, because to do so would remove the first and last line of defense in the imperial navy.
Moreoever, it fits with everything that is established about Palpatine and the sith (Rule of two), consolidating all power to himself, without any consideration given to what would happen should he fall.
Despite what the expanded universe might have you believe, he would have absolutely zero interest in a grand admiral Thrawn or any leader of the empire beyond himself or, at the very most, one of his sith heirs. Such an idea would likely repulse him every bit as much as a new republic because it would be someone he viewed as a “lesser” taking command of all that he had built.
Like or hate Episode III, the quote was extremely appropriate: “I AM the senate.” In Palpatine's ultimate view of the world, he IS the Empire. Without him, or a proper heir, there is nothing he cares to give consideration for. The entire empire can crumble into the dust for all he cares. This isn't even that out of line with the themes of the expanded universe which speculates that the loss of Palpatine's “battle mediation” force ability caused the imperical forces on endor to fall apart without his influence.
Adding this subplot would:
1) make it more believable that the empire could fall almost overnight as it seems too. In this version of the movie the capital would have been taken over and the backbone of their military has been obliterated, with nothing but the officers holding the bag. Not so crazy anymore.
2) make Anakin and what he does that much more important, because it cements the idea that without his final choice none of this would have been possible. The emperor would have simply killed luke and the rebels would have been crushed. Plus it also parallels his victory in episode 1.
So as for exactly what happens to the troopers once the emperor dies, I'm not 100% on how it should be handled, but my ideas include:
A) They die, instantly, falling over dead the moment the emperor is...... “shafted”.
B) They shut down, go brain dead, little more than droids with their memories wiped.
C) They lose the will to fight. A scene could be included with a stormtrooper laying down arms and an officer screaming “WHAT ARE YOU DOING!??! Fight to the death for the empire!!!!” and the stormtrooper could perhaps grab him by the collar, look him in the eye and go “What Empire? Who commands it exactly?”
D) Probably WAAAAAY too dark......but they commit quasi-seppaku. IE, they realize they've failed in their mission to protect their emperor, and so they take their own lives in penance.