The button mapping is hardcoded, afaik the DS even turn off the other buttons (or well, stops the hardware listening to input from them is probably a more correct way of putting it) together with other DS specific hardware components when going into GBA mode.
Perhaps a firmware hack could do it, but I seriously doubt it. If it was possible, Flashme would have it implemented already, it's not like you're the first one to ask for this :>
[edit] If you're a real badass with the soldering iron, and have worked some with SM components before, it would probably be possible to install a switch to physically remap the buttons. You'd have to find a really tiny one with plenty of poles though. I don't dare to guess how many poles you'd need since I have no idea how the controller circuit works. Basically it boils down to if you have to switch both sides of the buttons (if the signal is fed back to the controller chip(unlikely)) or just one (if the button just connects an input on the controller circuit to a power source or a ground connection (more likely))
[edit2] Forget the first edit, I misunderstood what you wanted to do first. A simple solution could be to just parallel couple the X button with the R button and the Y button with the L button. And of course you'd want a switch to break the parallel coupling too.
