Semmes was indicted in 1866 on charges of treason. Those charges were later dropped. Semmes was not indicted for piracy. That would indicate that the senior officials of the Johnson administration recognized that he was acting within the accepted bounds of Naval warfare. The Royal and the French navies seemed satisfied that Semmes was acting in that manner also. Had they believed otherwise there standing orders would have allowed them to pursue the Alabama as a pirate.
This business of "rebellion" was a carefully crafted legal fiction created for the sole purpose of lending some quasi legitimacy to the deliberate attack on another country.