I think if he were really being objective, from a species' survival point of view - or even a lost starship crew's view - a more human doctor might have chosen the "baby oven" over the "sperm donor." If you'll forgive the shorthand. As I'm sure the doctor was well aware, being programmed with virtually all of medical history, a mother having to make a choice between a drowning infant or toddler will more often choose the toddler, since it has survived the multivariate health risks of infancy. This is arguably a species-hardwired instinct.
In other words, all things being truly equal between the patients' chances of survival, a human would have made a certain kind of choice that a program, being PC (ha), did not make. The EMH lacked "gender bias." So you could argue it made him less human, in fact. Or at least less chivalrous, which, Harry certainly would have been.
It's not about inequality but survival of a tribe. All things being equal, how could you not
consider reproductive fitness? Yes, these were individuals, but they were also part of a starship crew on a lifelong mission. What kind of medical officer does not consider the long term impact on the ship and crew?
Ok, I know, they only have an hour to tell a story....