Play the exact same way you play on the Rebel’s side, but reverse all of the dice. You now roll purple and red die against the enemy’s green and yellow die. Use the classes the exact same way. And if you’re Jedi (like the Inquisitors), then roll up a Jedi per the usual and you’re off to the races. I think the only thing I’d probably change is when using the Force die (including the intro Force rolls), I’d keep that die exactly the same as before as it would create a few biases if you rolled for black on the die instead of the white. If this doesn’t bother you, then go for it! FFG SWRPG is made for fun, not sticking like glue to RAW, so test it out, modify as needed, and have a hell of a time. And if you need stats for a squad of rebels, just use the stormtrooper stats and so forth. No one will know but you, so who cares?!

Go get em, GM!