To take the documentation work out of most electronics rework, you can make your rework instructions a reference to the correct IPC document, revision, and section(s). Make sure a qualified person approves the rework. When it comes to verifying rework per IPC definitions, in most cases repeating the inspection that led to the rework is sufficient.
You may want to have your rework people IPC certified either to J-STD-001 Space, which requires a basic soldering skills test, or to IPC7711/7721 which is a much more difficult test.
Since the IPC defines rework methods, you can predefine what is and is not allowed, You can write into your quality system anyone with X training or certification is allowed to perform rework and document it. In my past experience, each serial number had a section inside the lot information in our ERP system that allowed quick tracking of rework.
I am wondering if you are making this more complicated than it needs to be. Is this in response to an audit, customer concern, or something similar. If yes, please post so the concern can be directly addressed.
Note FDA, ISO13485, and IPC definitions are somewhat different. IPC defines both rework and repair while ISO-13485 and FDA part 820 lumps the two terms together.
Tidge: It is very difficult to totally engineer out all possible needs for rework, as defined by IPC. Many medical products have too low a volume to justify the amount of engineering, equipment, and process development efforts required to engineer out PCBA rework.