I tried looking for the cheat codes, but I couldn't see one with the ability to lose player's settlement. So my best bet would be to indeed edit the files. Though notice that I've never done it before myself, so take my advice with a pinch of salt and always, ALWAYS back up the files you're editing.
In "<installation path>\Rome Total War Gold\data\world\maps\campaign\imperial_campaign" is a text file 'descr_strat'. In it you can edit the starting conditions of the campaign. Find a region called 'Attica' - that's Athens. Copy the whole section, i.e.
Code:
settlement
{
level city
region Attica
year_founded 0
population 3000
plan_set default_set
faction_creator macedon
building
{
type core_building governors_palace
}
building
{
type defenses stone_wall
}
building
{
type academic academy
}
building
{
type hinterland_farms farms
}
building
{
type barracks muster_field
}
}
and delete the current one. Next, find your faction leader, Kleomenes of Sparta, and paste the copied section above him. If you want to lose the settlements you don't want, copy all the settlements above this 'Attica' until begins the new list of armies, and move them to other factions. The rebel settlements are the last settlements in the settlement list, or if you want little challenge add them to Macedon's settlement list.
This only edits the owner of the settlement, next you want to make sure there are units in Athens. You find the armies have coordinates, and in order to have the armies in correct locations you need to know the Athens' ones. By going into the campaign map, and enter cheat code 'show_cursorstat'. It tells the coordinates of the point that is under the cursor. For example, Athens has 144, 52. So, say you want to have your faction leader to be located inside Athens. You find his coordinates under him like this:
Code:
character Kleomenes of Sparta, named character, leader, age 56, , x 138, y 46
Edit the x and y numbers into the ones you want, in this case x is 144 and y is 52. Likewise, later in the file you'll find there's an army that also has these coordinates. It's the rebel army that originally was located in Athens:
Code:
character sub_faction greek_cities, Demosthenes, general, age 20, , x 144, y 52
army
unit greek hoplite militia exp 0 armour 0 weapon_lvl 0
unit greek hoplite militia exp 0 armour 0 weapon_lvl 0
unit greek hoplite militia exp 0 armour 0 weapon_lvl 0
unit greek peltast exp 0 armour 0 weapon_lvl 0
Either delete them, move them to other factions, add these units to your amy by moving them to the list of your armies (not the character line, that's the general's info) or just let them be, as the game is smart enough to move them away from the spot without any problems.
You can of course add more units into the Athenian army, using the same form as the current ones have. I suggest moving your armies in the regions into the corresponding new owners of the region. The result is the more cleaner the more effort you spend in moving the units to the correct owners.