Are cities (by themselves) considered "enemy units"?
Not really.,. they can't block oposing units movement.
Can Player A drive some of his legions into the first of Player B's territories (enough to eliminate the legions there), NOT take over the city--then move his remaining legions to move PAST Player B's unconquered city to the territory behind it to attack the city with the temple (he just wanted to destroy the temple)?
Another example was Player A moved an army of legions through a territory of Player B's that had a city with two galleys in sea. Since legions don't fight galleys, can the legions move through the territory, decline to conquer the city, and continue into the territory behind the first?
Yes.. The galleys only become an issue if the player tries to conquer the city.
I guess my bottom line question is: can units move through a territory that is occupied by a city freely, or do you have to conquer a city in order to move through the territory?
Units can move through freely if there is no other units in the territory