Many people have accused Archer of hypocrisy in Cogenitor, especially given his own habit of sticking his nose into complex situations and deciding what is right. But if you do interpret his reaction as seeing a little too much of himself in Trip's actions - it makes total sense.
And I'll say the following as well - I still side with Trip, not only based on the morality of the situation but based on the fact that once the Cogenitor had decided it wanted a better life and once the society's real oppression of its Cogentiors was revealed, returning Charles would have been very dangerous because Charles had the potential to start a righteous rebellion. Even its suicide may well have served as a beacon to other disgruntled Cogenitors and caused a rebellion that the society wasn't ready for.
And I don't blame Trip either. If you visit a culture that prides itself on equality and parade around your sex/procreation slave, spew delusions about its intelligence and value and in general act like douches - don't be surprised if someone sympathizes with your slave and tries to help it. It would be an entirely different matter if Trip misunderstood the situation - but there's no evidence he did. His mistake was not understanding the consequences of his actions, not being wrong about Charles being oppressed.
So, I definitely think that deep down, Archer sees himself in Trip's actions - and realizes that it could have been him that caused the tragedy. That's why he comes down so hard on Trip.



