On the one hand you have an issue with Archer's lines from the end of Cogenitor but on the other hand you think that Trip messed up?
Anyway, back to the main issue, I like your point that the Vulcans involuntarily influenced humankind. What I don't like is the use of the word evolution only because Phlox used it in the episode. It's about the social relationship between two species, not about their biological fundamentals.
You claim that not helping when help is asked for is as wrong as helping when no help is asked. This assumes a pretty naive picture of the world. Take any group which has fought an emancipatory struggle in history, they first have to convince their brother and sisters. Workers had to fight bourgeois ideology, blacks had to convince the Uncle Toms and women had to convince the all-too-happy housewives.
In "Marauders" Archer first has to convince the workers that it is worthwhile to fight against these bullies who steal their property and you claim that this is essentially a violation of the Prime Directive.
But you consider it not merely totally acceptable but even mandatory to help one species on a planet which asks for help but not another one which is obviously kept back merely because the former one explicitly asks for help while the latter does not.
Suppose you knew a woman who is regularly beaten up by her husband. You offer your help but she refuses. Obviously you should help her against her will.
People can be influenced by ideology, fear repercussions of resisting or just be happy in a subservient position, be it housewives, Uncle Toms or Menk.
If you help the Valakans you gotta help the Menk, thus becoming something far worse than an imperial force. That's why you can help neither. Phlox, while sometimes appearing to have a bit of an ugly social Darwinistic mindset in this episode, clearly realized this. He neither shares humankind's urge to help the Valakans nor humankind's sympathy with the Menk but he realizes that the two human gut reactions are in conflict with each other and comes up with the right solution.
So cruel indifference is now a form of morality in the Star Trek Universe? I hope not.
So according to this logic, was it okay that West did nothing well there was a genocide in Rwanda in 1994? Many people think the West's inaction was immoral at worse, amoral at best, no one really thinks it was moral.
In Rwanda, the Hutu extremists used the fact that in the past the Tutsis discriminated against them as an argument to justify committing genocide against them. Two wrongs do not make a right, you cannot use evil acts of the past to justify present evil acts.
To say because Valakans were mistreating the Menk, somehow justifies letting them die in a plague, seems very immoral. The US had slavery in the past, would that justify allowing the entire US population to die in the 19th century? What about Germany, because of the crimes that nation state committed in the past, does that mean no one should help them if there was a plague there? Why should we assume that the Valakans would always mistreat the Menk, how would we know the Valakans would make reforms in the future? Also frankly the Valakans seemed far less brutal then either the US or Germany did in the past, so why are they less deserving of help? Also why should Valakan children be punished for the sins of their fathers, how do know the next generation wouldn't have changed things? I don't see anything the Valakans did as a justification letting them die.
In this episode Archer replaced compassion with cruel indifference. That doesn't seem moral, it seems psychopathic. I don't care how far in the future it is, being compassionate is part of being human, being cold and indifferent makes someone seem less human, more like a robot. To say indifference and callousness is superior to compassion, sounds really screwed up.