How can I change this behavior so that it only downloads the runtime if necessary?
From the 6.2 Release Notes:
31206: When an installation was run with WebDeploy, and was configured to pre-install the .NET Framework, it would install the .NET Framework even when it was already on the destination computer. The code has been modified to check the version number before installing the .NET Framework. However, because of the way that Microsoft stamps their update versions, the DotNetFX.exe file must be downloaded before the Wise code can check the version.
Update: This has been fixed for Wise Installation Studio 7.0.