Hello, MikeDouglas,
Mage should not make you uncheck the deploy option. If you don't have the deploy option selected, and the files renaming as .deploy, you will find it very difficult to find anyone who will install your application, because their firewall will most likely stop any .dll or .exe files.
And for God's sake, I wouldn't try to figure a workaround on your webserver for this; you'll open up yourself to all kinds of security risks.
Just my two cents' worth.
RobinDotNet
Click here to visit my ClickOnce blog!