Some of what I say may have already been said but, in my experience, I have often found that changes to software or software baseline results in the majority of unexpected issues with security. While a modeling program like that may help, especially with planning out your network layout, I'm not so sure it would really help much with security. If your issues are port specific, I know that some security software have learning modes that can analyze port traffic and lock down ports based on its analysis. If any changes occur to the software, you can just re-enable the learning mode.
I think the most surefire way to alleviate some of the issues is to test proposed changes to software in a mini, non-live environment before making it go live. This, of course, would have to be coupled with documented test procedures.