The quick answer is to have a quality assurance group that does security audits on any application or service added
to the infrastructure. In reality it's a matter of defining a security strategy and the appropriate testing standards that can be applied to any service being implemented. A good start is to test the application against the Open Web Application Security Project (OWASP) Top 10 application risks. This list identifies the most common deficiencies found in application deployments.
In addition, you should work with your compliance and security organizations to include other tests based on your organization's requirements: For example you might need to do a PCI self-assessment if the application in question handles credit card information, or a HIPAA review if you deal with health care info. There isn't a one-size-fits-all Windows Active Directory security configuration assessment, but between OWASP and your security team, you should have a good list to build from.
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