Medical assistance which sustains a system of oppression is already a crime among humans (if Hitler is sick your ethical injunction is not to cure him but to ensure that he dies) and definitely among aliens.
Except this would akin to not giving medical assistance to all Germans because the crimes of the Nazis, not just Hitler. Phlox and Archer not only condemned the Valakians leaders who were oppressing the Menk, but all Valakians. That would include innocent Valakian children and Valakians who would be trying to help the Menk. Letting the innocent die along with the guilty is unspeakably callous and it makes Archer inhumanly cruel.
Any sort of enlightenment without basic human compassion, just comes off as psychopathy, instead of evolving into something better, Archer just comes off as someone who has lost his humanity completely.
It is not a matter of being guilty or innocent or even responsible. The master-slave / parents-children relationship between Valakians and Menk has been deeply burned into them over, assuming that these two species have existed roughly as long as we have, hundreds of thousands of years. It is totally natural for them and, siding with Phlox, I hesitate to condemn this in anyway.
But we do not assume what you call the psychopathic but the human, compassionate perspective, compassion with both species.
Having compassion for both and then playing pick and choose seems tyrannical to me.
So we can help none, some or all; we can be sociopaths, tyrants or gods. I wish there were an easy solution which makes one feel good but alas there isn't. Whatever you do is, as often in ethics, a monstrosity.
If there was any ethical injunction for the generation of my great-grandparents it was to do what is normally wrong, take a life, kill Hitler. About Japan, I do not know whether nuking or fighting on and loosing many of your own men was right. Again a horrible ethical choice.
Or, to pick a slightly more funny fictional example, McNulty faking homeless murders in the last season of The Wire was obviously wrong from a legal point of view but in my opinion tricking the ill-functioning institution into doing the right thing, provide more manpower for the drug case, was a sublime ethical act.