I've not experienced this yet. If/when I do, I'll have the person I give my keys to -- TSA or airline employee -- SIGN a note with their name, employee ID or badge #, and position. That way, if there are any discrepancies at my destination, I can file a claim with that info. It avoids TSA and airline employees pointing the finger of blame at each other:
"TSA took the keys from the passenger."
"No, TSA received the keys from the airline rep."
My note would show who took control of my keys, making them and their employers responsible for safeguarding my property.
They can't force us to comply with policies and then deny responsibility for losses caused by their policies.