Namor was wrong.
In your defense of him you assume a utilitarian ethos which pursuits “the greatest good for the greatest number.” If such were the correct moral principle, then such a conclusion would indeed be correct.
I argue, however, that a deontological ethos should be followed in moral decision making, in which all moral actions are considered in a vacuum. Thus the question “Is it wrong to murder a populated world” can never be qualified with “in order to….” The action is wrong, in and of itself, and therefore ought not to be committed.
A deontologist solves the Trolley problem by distinguishing between active and passive deeds. The act of preventing a trolley from running over five individuals is morally commendable, but not morally obligatory. The active deed may be praised, but the passive deed of allowing the individuals to die cannot be condemned. Inversely, when the active deed itself constitutes murder, as in the cases of switching the lever or dropping the fat man, then the active deed becomes morally condemnable, while the passive deed remains morally neutral, as in the first case.
When the Illuminati save one or more worlds, their actions are morally commendable.
When the Illuminati murder a populated world, their actions are morally condemnable.
When the Illuminati fail to save or murder a world, their actions (or lack thereof) are morally neutral, on the exact same moral level of everyone else on Earth-616 who failed to act in regards to the incursions.
The fate of the world is NOT in their hands, but the state of their souls IS in their hands. And the latter is infinitely more valuable than the former.