Are you talking about hearthstones? Or a separate stone which teleports you different places that you define?
As for changing the faction of the portals. You can change the factions of game objects with this query I've made for you.
This one will make it horde:
Code:
UPDATE `gameobject_template` SET `faction` = "2" WHERE `entry` = "put the object entry here"
This one will make it alliance:
Code:
UPDATE `gameobject_template` SET `faction` = "1" WHERE `entry` = "put the object entry here"
This one MIGHT make it neutral, haven't tested it though...:
Code:
UPDATE `gameobject_template` SET `faction` = "120" WHERE `entry` = "put the object entry here"
entry = ID
You can find the id by typing .lookup object in game
Hopefully that helped =P