I think part of it also stems from our "colonization" of other species on Earth.

We exploit the living shit out of every other living thing while telling ourselves those living things are somehow different from us, don't experience the same fears, the same pains, and so on. Those of us with an inkling of self-reflection can see how they are like us just by looking at how they react to similar stimulus. We aren't different but we've spent a millennia telling ourselves that we are simply because we have language and can create tools. Both things other animals clearly have and do, but since we don't understand those animals, instead we treat them as inferior.

I think part of the panic of colonization of other species comes from the deeply rooted realization that we have been brutal, violent executioners of millions of species who may have had similar reasoning capabilities as we do but simply don't have thumbs so they can do things like write down their language or codify it in any way. Like how humans lived for millions of years without written language...

Anyway, yeah, visceral guilt for being real fucking bastards and killing off so many species that we literally kicked off a mass fucking extinction.

I feel like the show does a good example of being entertaining while also showing those stark contrasts between the civilizations like you've commented. Even more so in the later part of "Stargate Atlantis" where it's more "cowboys and indians" style. They're trying to "save" all the planets in the Pegasus galaxy but tend to shoot anything they don't understand and constantly undermine themselves by making poor decisions when it comes to relations and dealing with people. The inhabitants of the galaxy have continued being successful at trade and socializing (except for a few outliers who can still be known to show honor) even while being under constant threat for their entire recorded history.