Okay, so the title may have been a little misleading. I'm not going to show you how to avoid warning CA0060, but how to avoid your build failing because of this warning.
This is only helpful if you are running FxCop as a Post-build Event. When FxCop fails due to its inability to find indirectly referenced assemblies, it exits with error code 512 (0x200 - Assembly Reference Error). So all you need to do is check that error code, send out a simple warning message, and reset the error code to 0. The following can be placed directly into the Post-build event field in your project's properties.
<YOUR FXCOP COMMAND>
IF 512 == %ERRORLEVEL% (
echo postbuildevent:fxcop warning FXCOP:FxCopCode analysis was unable to complete.
SET ERRORLEVEL = 0
)
The echo is formatted so that the warning will show up in Visual Studio's Error List. See my other post for more info on how that formatting works here.