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Two options that spring to mind:
1) symlinks. Make 2 directories for addons. WoW will look to {root}/Interface/AddOns for your addons. If you were to write a script to change a symlink from {root}/Interface/AddOns which points to {root}/Interface/AddOns_User1 or {root}/Interface/AddOns_User2 or back. This could be done at login or by creating two links to start the game and executing the symlink change before loading the game.
2) AddOns.txt. As with the symlinks you could execute the changes to the needed files at login or with a shortcut. The AddOns.txt file has a list of addons and determines which ones are enabled or disabled. Replacing the file with the list of AddOns you want for user1 or user2 will allow you to start the game with the appropriate AddOns loaded. The AddOns.txt file is located in {root}/WTF/Account/{account_name}/{realm_name}/{character_name}/AddOns.txt.
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