Best way to deal with this turned out to be changing the controls for up/down and left/right. Instead of arrow keys, I use I/K, J/L respectively.
In /lib/apps.js:
switch(event.keyCode){
case 73: // UP
callback(player, jsnes.Controller.BUTTON_UP); break;
case 75: // Down
callback(player, jsnes.Controller.BUTTON_DOWN); break;
case 74: // Left
callback(player, jsnes.Controller.BUTTON_LEFT); break;
case 76: // Right
callback(player, jsnes.Controller.BUTTON_RIGHT); break;
And in /shortcode-template.php:
<tr>
<td><?php echo __("Left"); ?></td>
<td><?php echo __("J"); ?></td>
<td><?php echo __("Num-4"); ?></td>
<tr>
<td><?php echo __("Right"); ?></td>
<td><?php echo __("L"); ?></td>
<td><?php echo __("Num-6"); ?></td>
</tr>
<tr>
<td><?php echo __("Up"); ?></td>
<td><?php echo __("I"); ?></td>
<td><?php echo __("Num-8"); ?></td>
</tr>
<tr>
<td><?php echo __("Down"); ?></td>
<td><?php echo __("K"); ?></td>
<td><?php echo __("Num-2"); ?></td>
</tr>