I don't see much point in trying to override the csproj settings with a different set - surely you want to use the same CA settings (or disable CA entirely) whenever and wherever you build the code?
As foosnazzy says, there's (usually) no need to do this in MSBuild. You can use the CA check in policy to set up the rules you wish to apply. Then, right click your solution in the solution explorer and about half way down the context menu there is a submenu of options for applying the TFSProjects' CA policy to all Projects in the solution. You can overwrite the project settings with the server's, or merge them.
It may only copy the settings for the current configuration so you may need to do it twice if you want to apply the same CA settings to Debug and Release. (I vaguely remember this happening but we don't run CA on our release build so it's not something I've tried recently)
(This was available in VSTS2005, but it didn't work - the values were "merged" with those in the projects so that any existing CA rules would be increased in severity (to warning or error) but you couldn't disable CA rules (demote error -> warning -> disabled). In addition, every time you opened a solution the CA settings would "drift" so that you had to reapply them every few days to keep it working)
An alternative is to set up the CA rules you want in a single project, find the XML element that contains the list, and use a text editor (or a few lines of C# code) to do a global search & replace for the CA element in all csproj files in your project. That's how I did it until VSTS2008 came along - once you've sussed the technique it only takes a few seconds to migrate your settings through all the csprojs. The advantage of this is you can be more selective about which projects the CA rules are applied to.