I don't have a Macbook running Bootcamp to test this right now, but as I recall, there's a setting for where on the touchpad the right-click zone should be, which is separate from the setting for the mouse right/left buttons in the Windows control panel. Click on the Boot Camp icon in the notification bar, and select "Boot Camp Control Panel". There should be a tab for touchpad settings; use this to select a different touchpad right-click zone. The right/left settings for the external mouse should remain the same.
Here is a screenshot of what the boot camp control panel options should look like. Right where it says "Secondary Click" on the lower left, you can use the dropdown menu to change it from "bottom right corner" to "bottom left corner" or vice-versa. If this option does not appear, you may need to update your bootcamp drivers, which you can do by downloading the most recent bootcamp updates from Apple.
You should be able to set your mouse settings in the Windows control panel to be for a left-handed mouse, then set your touchpad settings using this method to be right-handed.