As far as the payments to the donor and agency, it depends on how the contracts were set up. In ours the donor got incremental payments at certain milestones, such as passing clinic medical clearance and starting injectable stims. Since your clinic did accept her and she started her meds and went to monitoring appointments in good faith and compliance, you probably do owe her some compensation, how much should be spelled out in the contract.
I don't understand why your clinic even accepted the donor based on AFC of 3, that seems outrageous to me, and costly.
The agency will probably also want to be partially compensated since the cycle did officially get started, and they aren't really responsible for poor response
The remainder of the agency fee they usually want to apply toward another donor from the same agency.
Maybe you can get the remainder of the donor's expensive meds, but I don't know if that is even allowed.