Yes, this is possible. With multiple prepayment options for specific properties, a Travel Agent can pay the reservation in advance. The customer pays the Travel Agent and the company credit card/Paypal/Bank Account is charged. The Travel Agent clearly has to communicate this to his/her customers, and still needs to provide a confirmation document (with confirmation number and pin).
A Travel Agent also has the option to make a reservation and contact the property to request a prepayment for that specific reservation.