The rebels have overthrown the Empire. What do they do with all the Imperial stormtroopers, officers and crew?

Many of them defect, many try to become little figureheads leading to Imperial infighting.

Admiral Thrawn unites many of them at one point, I haven't kept up with the novels so I'm not sure what's going on in the New Jedi Order.

thew them into pow camps where rebel solders abused them. When the pictures came out, the rebel solders were put before the new republic.......media frenzy.