Good question Dallas. Sometimes policies are unable to cover everything. Could the policy driver for not going back retrospectively be more about new applications (as opposed to cases like this one)?
Go with your instincts and if that is to provide the rebate retrospectively to ensure seamless entitlement in this case (so long as you have evidence of eligibility which I believe you do have), seek a once off decision outside of the policy and document that decision. Does your policy have a statement about a certain officer of council being able to vary the policy from time to time?