There should be no rule language that states you cannot noncombat move through a seazone (or territory) that has been cleared during the combat phase.
As long at the carrier was not moved and was not involved in combat during the combat phase, the carrier is allowed to move through any empty space during the noncombat phase. If the planes didn’t succeed in emptying the seazone of surface warships, then the carrier could not move into the seazone during the noncombat phase.
Additionally, subs and transports don’t make a seazone hostile, so the carrier could move through seazones that only contain subs/transports.