.csproj.user issues when checked into TFS
I also wanted to check in .user files to do what the asker wanted, to provide defaults for the debug/run options. It turns out that the .user file is just another MSBuild Project XML file, and you can just "merge" the property group in there into your project. No need for .user files.
<PropertyGroup Condition="'$(Configuration)|$(Platform)' == 'Debug|AnyCPU'">
<StartAction>Program</StartAction>
<StartProgram>$(VS100COMNTOOLS)..\IDE\devenv.exe</StartProgram>
<StartArguments>/rootsuffix Exp</StartArguments>
</PropertyGroup>
Make sure no one has the file checked-out then delete the file - checking in as a delete and not an edit.
I use Team Foundation Power Tools and do it from the Windows Shell Context menu
I suggest that you use the Destroy command. Be careful since it deletes permanently. MSDN documentation: http://msdn.microsoft.com/en-us/library/bb386005.aspx
Start a Visual Studio 2010 Command, and use tf.exe ...