I couldn't find any pages on silently installing the windows phone desktop app. The file is downloaded as an exe and the /s -s or /silent or -silent don't appear to work.
http://www.windowsphone.com/en-gb/How-to/wp8/windows-phone-app-for-desktop
However if you want a silent install you can retrieve the msi file by running the exe, the msi can then be found in C:\ProgramData\Applications\Cache mine was titled {E786AE85-8A30-4CF2-BF70-57404A5CD684}v1.0.1720.1.msi
You can then just use msiexec /i "{E786AE85-8A30-4CF2-BF70-57404A5CD684}v1.0.1720.1.msi" /qn
