A classic example of double speak. It seems the priest backpedaled once he saw you were familiar with the Church's teaching on this issue, but his proviso makes no sense. The Catholic Church condemns acts of direct abortion as always gravely sinful. The chaplain knows this is true (if he does not, he received radically defective seminary training or is intellectually incompetent and should not hold the position of chaplain), even though he chooses to flout Church teaching and sanction the dispensing of the "morning after" pill, an abortifacient drug. The "morning after" pill is not a contraceptive--it does not prevent conception--its only purpose is to induce the abortion of an already conceived child. Therefore, its use may never be regarded as a morally acceptable option, even under the principle of double effect.
The chaplain's stipulation that the abortifacient should not be administered in cases where "the woman thinks she might be pregnant" boggles the mind. What purpose would this serve? Does he realize what the "morning after" pill is? Does he understand the Church's teaching on abortion? If he does, then he is dissembling. If not, what's he doing as a hospital chaplain?