Yes you can. The SECG state:
If the amounts paid by the consumer at closing exceed the amounts disclosed by more than the applicable tolerance threshold, the creditor must provide a corrected Closing Disclosure and provide a cure for a tolerance violation no later than 60 calendar days after consummation. The refund need not be in the form of a cash refund to the consumer.
Creditors can cure tolerance violations in many ways. For example, a cure for a tolerance violation can be provided by:
Providing a refund directly to the consumer;
Providing a principal reduction;
Providing lender credits, either specific or general, to the consumer.
You will need to follow the instructions outlined in 38-4 for how to disclose the principal reduction on the CD you will send to the borrower.