You can add the ALT+Key to the KeyClone do not pass list which means it will cast on whichever one is in focus and not the other one.

Or you can modify the macro several ways (only on 1 character).
All modifiers:
Code:
/cast [target=focustarget, nomodifier] Lightning Bolt
Alt:
Code:
/cast [target=focustarget, nomodifier:alt] Lightning Bolt
or:
Code:
/stopmacro [modifier:alt]
/cast [target=focustarget] Lightning Bolt