The American revolution might be the exception that confirms the rule, since the new regime (Congress and the President) seem to have not persecuted, legally or extra legally, any Americans or their allies who fought against Britain after the war was won. I at least could not find any examples of this. Benedict Arnold doesn't count since he did, beyond any doubt, commit treason against the revolution and rightfully was persecuted for his actions.

Cromwell's station in the revolution of Parliament against king Charles was very minor during the first half of the civil war. But he rose to prominence and thereafter many of his former allies were persecuted (with the exception of lord Thomas Fairfax).

Castro persecuted many of his former allies after Batista was ousted from Cuba, including Manuel Urrutia Lleó and Huber Matos Benítez (and also maybe Camilo Cienfuegos Gorriarán, since his accident happened during a very convenient moment)...

Stalin. REALLY???? He had Trotsky killed two continents away and more communist party members died because of him than because of the Tzar!