So, your commander is being a bro here. Your unit security assistant (previously known as manager) is obligated to report these things but if the CC is trying to handle it, they're on shaky ground by even offering to accept a rebuttal in order to not report it.

The CC is a custodian of the classified information within their purview and thus can only suspend access. Can't take away your clearance or even suspend it. Just the access to the info/ systems.

Anyways, best to show some sort of documented plan to get things under control. The A&FRC has budget counseling and you can walk out with papers in hand to show that you're on the up and up.

Seriously, be grateful your commander is shielding you from the CAF and keeping your record clean and again bear in mind, they don't even have the legal authority to do so.