In my opinion, what is needed is not so much a commission about Cast Lead. Instead, there should be an independent audit of the IDF investigation processes and procedures.
Auditors know how to check not only whether the processes and procedures are effective (in this case, for investigations) but also whether the IDF is accurately following their own procedures. If the audit comes out clean, then the IDF procedures would be "certified."
These external audits should happen regularly, perhaps annually. They can be done by a Big 4 accounting firm without compromising Israeli security. They should happen regardless of any political events like Goldstone. They should not be done to mollify the world, rather to ensure to the IDF and the GOI that IDF procedures are effective, fair and accurately followed - which should be welcomed by all.
This would solve all the problems. If the audit comes up clean, fair minded people can look at the sanitized results of the report certifying that the procedures are valid just the way that audit firms validate all sorts of procedures. If it doesn't, the IDF and the Government of Israel would be the first to want to know how to improve their procedures.
An audit procedure would address the root issue - whether IDF investigation procedures are adequately independent, effective and adhered to. Instead of spinning up a commission for every alleged war crime that some NGO screams about, this would be a reproducible, self-correcting and certified process that is used by major corporations daily.
It is entirely possible that the IDF does this already, but if not, it should.
(I briefly discussed this idea in a comment on this blog, and I sent it to a mailing list with really smart people, and no one responded. So either it is a brilliant idea or it is incredibly stupid.)