Ok, don’t write to me about the ways to get around this security method, I get it. However, this is a cheap method for some easy security measures. Plus, using source control is what every programmer should be in a habit of doing. This also makes wordpress core updates very easy to do.
1) Create a repository and check in wordpress. Yes I realize wordpress already has a repository but this way you have the option to update when you are ready.
2) When you need to build a wordpress site, check it out from your repository.
3) When a new wordpress core version is released, you can update one of your instances and commit it back. You can then svn up all your instances.
4) use svn status to see what if any files have changed. If an exploit changed any wordpress core files, you will see a modification next to the file. Simply delete, svn up, and make sure you patch your source.