Your shooting yourself with this, imo. ONLY IT pros that have access to the code. Maybe I am wrong, tell me so.
Well yeah, but that is always so... I am accustomed to lockdown conditions for Chain of Custody purposes... with a knowledgeable IT guy looking over my shoulder at every moment. Same goes for hard drive destruction...
As far as the code itself - the finished software would be in an installation package with an m5d checksum provided - The initial software is thus tamperproof. The working software, less it's configuration files, will also be testable in it's various parts according to file size and dates. I do this all the time with operating system files to see if they've become corrupt, or some outdated .dll file didn't get replaced...
Configuration is another thing though, as those files change by their nature, but can be captured at a specific time (like upon certification)... and a 'picture' taken of the software, or the whole dang machine to have a sure record of the machine and software state at the time of cert.
So no, it is pretty hard to change a forensically recorded system.