@madvitale
There is a game option "Transport Casualties Restricted", which would allow transport units only to be taken as casualties last after all other attacking/defending units are removed. It's for version 3 rule set, where Transports attack and defend at 0. WaW follows version 2 rule set as Transports defend at 1. Also, WaW does not have this property. To add the property, open the WaW xml (World_At_War.xml) in a text editor, search for 'propertyList' and add the following:
<property name="Transport Casualties Restricted" value="false" editable="true">
<boolean/>
</property>
Now the setting can be changed under 'Map/Game Options'.
Cheers...