I think once the client loads eqclient.ini, any further changes to the ini won't actually modify in-game bindings without a relog.
Following this logic, you could probably write a simple batch script to swap between two eqclient.ini files. Realistically, this could be added as a subroutine to the batch file that is used to launch the game. Make two of them and you have two desktop shortcuts to click, one for each account.
Edit: Nevermind, I skimmed and didn't realize you meant characters on the same account. You could still achieve this using the above method, but you'd have to do a full client reload every time you switched toons. Kind of a pain in the ass.
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