I have found a temporary workaround in which I created a dummy dll that removed all functionality from exported vis but had the same name and function signatures. I then built the application using this dummy dll. Once complete, I replaced the dummy dll with the real dll.
This is not a satisfactory work around because we have to build and maintain two dlls. Also, I'm not sure we can do the same trick when creating the installer with application builder. So, I'd still appreciate any help you can give.