So what Marshall and Kenny said was right - presently you cannot move through a friendly faction's sea zone. This is from the friendly faction's paragraph on page 4:
For almost all purposes, friendly factions interact with one another as if they were owned by separate players. They... cannot share control of spaces, and they cannot move through one another's spaces.
Now while it intuitively makes sense why we didn't allow for dual occupancy of territories (its not too hard to think of all the complications it might lead to) you might wonder why we don't allow for dual occupancy of a sea zone, or at least for the bonus sea move to allow for a "move through" function, so long as all the moved units end the turn on a different space than the friendly faction's space. The reason was, its possible that the bonus sea action might be an attack - in which case, if a battle was called off before that space was conquered, those failed attacking units would then be left occupying the sea zone with their friendly faction.
This leads to the question why not allow for dual occupancy of sea zones? There are several problems - for instance, if the sea zone was attacked, which defending units would die first? Does the attacker choose the causalities or the defender? If cards were played on behalf of a defending faction involved in this conflict, how is that handled - for instance, if Special Forces is played, does it only cover faction A or faction B or both? Of course, rules could definitely be created to handle these situations - but we felt that this level of additional complication was beginning to move beyond the spirit of the game.