We are also facing the same issue. I don't see our team running every single time FxCop as a command line (even in the "Build event"), as we have already too many quality tools and rules. Moveover, this would mean changing manually 300 csproj, and test for non regression...
Therefore, we stick so far to SL4, but it presents some other major side effects, such as new components on SL4 does no behave the same way in SL4.
We might just end-up disabling all CA and use third-party tool.
<CodeAnalysisAdditionalOptions>/directory:"$(ProgramFiles)\Reference Assemblies\Microsoft\Framework\Silverlight\v4.0" /directory:"$(ProgramFiles)\Microsoft SDKs\Silverlight\v4.0\Libraries\Client" /directory:"$(ProgramFiles)\Microsoft SDKs\Silverlight\v5.0\Libraries\Client" /directory:"$(ProgramFiles)\Microsoft SDKs\RIA Services\v1.0\Libraries\Silverlight"</CodeAnalysisAdditionalOptions>
<CodeAnalysisPlatformPath>$(ProgramFiles)\Reference Assemblies\Microsoft\Framework\Silverlight\v5.0\mscorlib.dll</CodeAnalysisPlatformPath>
Code Analysis now runs within Visual Studio for us. This is similar to one of the comments in the Workarounds tab, except we didn't need to change any shared files.