It's a deliberately nuanced and ambiguous moral dilemma, and some people want everything to be clear-cut and black-and-white. "Tuvix" gets the same kind of heat for the same reason.
Although to be fair, "Dear Doctor" is flawed by its implausible evolutionary premise that an entire species can have a finite life expectancy programmed into its genes. It was trying for a sci-fi analogy with end-of-life care and how medicine is sometimes about accepting and easing the inevitability of death rather than fighting it. But since the analogy of individual death to species death didn't make much sense, it weakened the case the episode was trying to make, and lent itself to misunderstandings.
I can shrug it off because it's an alien species and maybe evolution does work that way there. Hypothetically, if a planet's evolutionary process had some kind of built-in apoptosis on a species level, if species dying off on schedule to open a niche for new species were necessary to its balance, then you could fairly ask whether disrupting the process to save lives now would harm far more lives in the future, and whether a single starship captain has the right to take on that burden without a lot of serious debate with experts, scientists, philosophers, and policymakers first. You have to be willing to buy into that implausible hypothetical first, but to me it's no more absurd than humanoid aliens in general, interspecies breeding, telepathy, evolution into energy beings, etc.