When you bind anything to mouse 2 it doesn't change secondary fire for dual wielding. You have to edit the actionmaps file in My Documents\My Games\Crysis Warhead\Profiles\Default
You change
<action name="attack2" onPress="1" onRelease="1"> <key name="mouse2" />
to
<action name="attack2" onPress="1" onRelease="1"> <key name="mouse3" />
or whatever the desired key is