If these events had occurred in the 24th century and a Starfleet officer had done what you suggested, interfere into the relationship of two alien species and give one an advantage over the other, he would have been court-martialed for having violated rule number one.
I agree though that Archer's choice is immoral. Interspecies ethics runs counter to the natural, biological morality of some stupid primates which is precisely why these stupid primates needs those new ethics so direly when they wade into deep space.
It's not "giving anyone an advantage." It's keeping them all from dying when it costs you absolutely nothing. Picard stopped a geological disaster in Pen Pals on those grounds even though it broke the Prime Directive. Heck, every Starfleet captain that's had a show has broken it several times. None of them got court martialed.
I'll agree that the Valakian social system leaves something to be desired, but letting them die off? Heck 200 years ago in our culture it was legal to own a person as a slave based solely on the color of their skin. We improved for the better, and by all accounts the Valakians weren't even so malicious as we were. So it stands to reason so could they. Too bad they never got the chance.