I disagree with your conclusions - if the previous Thargoid interactions were Thargoid Wars I, then this could be considered the beginning of Thargoid Wars II. As with the two World Wars, the actors and motives involved were at least a little different and where the Thargoid incidents are involved now there is no substantial evidence to prove your conclusions. We do not know if who/what we are dealing with - we know they are Thargoids but not the controlling body/bodies nor their explicit intent.
You need to study your history better. World War II was really World War I PART 2, as in the first directly lead to the second. The reparations demanded by the allies (excepting the US, which was firmly against that) plus the economic damage done by the war, directly lead to Germany militarizing and annexing countries. As for the Japanese, they never stopped their expansions/conquests started during the first World War, but not really considered part of it. I say all this having taken a 400 level course on US Military History (all of it up to Desert Storm), a 500 level course on the Pacific War (1930-45), and studying WWII as a hobby. The reason there wasn't a World War 3 twenty years later was that US spent a lot of money rebuilding both Europe (Allies AND Axis countries) and Japan, which is the first time in history a victorious country has rebuilt a conquered ones and not occupied them.
As for painting all the Thargoids with the same brush - they're a hive minded species! I'm sorry this hasn't been explicitly demonstrating to you in game yet, but that's the way it is.
Tarring all Thargoids with the same brush as the Thargoids that humans previously encountered (a long time ago) is just demonstrating xenophobic patterns of thought given that we are led to believe that the Thargoids are not just one faction. How would people like it if all humans were considered hostile megalomaniacs intent on world domination/destruction just because of a handful of individuals who might think/act that way.
Xenophobic? I was willing to give them a chance even AFTER they attacked that Federation convoy, which finally identified them as Thargoids. Then they proceeded to attack Federation, Imperial, and Civilian targets AND abduct survivors! At that point, yeah, I joined the camp that is for giving them a bloody nose.
Oh, and the Thargoids don't paint us all with one brush because they know we act as individuals. Again, this definitively highlighted in several of the books.
To try and keep things in perspective, you dismiss morality as if it does not matter but it always matters... it is what separates humans from animals, take morality out of the equation and the resulting actions are no longer humane. Sometimes atrocities are justified in the name of preventing a greater atrocity but it does not mean that there are not viable alternatives that could avoid any form of atrocity.
When it's the survival of our species, or theirs, and they're the ones encroaching, it's pretty simple. But if you want to keep equivocating and all that, fine. If the mycoid virus hadn't been used years ago, we wouldn't be around to have the discussion now.