He wasn't programmed to cry.
If you asked him, not that you would've, Dr. Zimmerman would have said that crying represented a malfunction in the Doctor's subroutines, a digression representing a larger problem. Because he wasn't programmed to cry.
But then again, he wasn't programmed to have feelings either. He was programmed to view all patients with a professional detachment, treating the symptoms, not the person. Why, then, did he look down at the withered husk that was once B'Elanna Torres, and find himself suddenly unable to perform an autopsy?
He was…disappointed. No, that wasn't quite right. Angry was closer, but he knew it wasn't that. He had seen anger, desperation, in Tom Paris as the medic watched his wife's life drain away before him. Anger that manifested itself in futile actions. The Doctor wasn't angry, not exactly. He was….sad. Yes, that was it. He was unbearably sad.
He wasn't programmed to mourn. He was supposed to accept the deaths and move on. But that was impossible. Instead, the Doctor, the one who wasn't programmed to cry, sank into a chair at B'Elanna's bedside and let the tears flow freely down his face.