How do I reduce the amount recorded on a payroll source deduction payment to accommodate a penalty refund to our CRA account?

Create a bill credit for your CRA tax vendor.  When you go to pay your next remittance, pay the positive bill for the remittance and the credit bill, and you will end up paying only the net amount.  Of course you have to file the whole amount for the current remittance, but once you apply the credit to the account, your payment will only be the net difference.