It's most likely so that western media has always framed "da nyatzis" as the bad guys of ww2, irrespective of what branch of the armed forces they belonged to, or whether "da nyatzis" were even fucking soldiers. I can understand saying this about the Waffen-SS as a whole, and for them you could make a better argument towards that, but even THEN that isn't fucking true for the entire organization (see Nordland and the Baltic units). Westerners have been taught to percive anyone who uses a German-esque aesthetic as the bad guy and they see little nuance in Gundam because of that.
Zeon are the bad guys btw, Earth #1.
It's also worth pointing out that Amuro gets mostly carried by his machine before he starts to understand the people he's fighting against. This trend reverses with Ramba and only escalates as the OYW goes on, culminating in Amuro carrying the Gundam. This carrying of the Gundam coincides with him meeting Lalah, as well.
Before that point and before meeting Ramba, Amuro goes on a fucking rampage murdering retreating Zeeks. It's one of the more interesting moments of the series and arguably pulled off what Thunderbolt 1 was trying to do years later much better than Thunderbolt 1 did.
I say this because I found myself going from cheering on Amuro to being a little shook watching a 15 year old go totally berserk and hunt down enemies fleeing in terror.
While watching Thunderbolt 1 I just got the impression that the creators really really really REALLY wanted me to understand how terrible war is; as if I needed to hear teenagers screaming at the top of their lungs while they're being killed (which is fucking dumb anyway since the feddies mostly use officers as pilots anyway but nevermind that) to understand that war is bad.
I think I gleamed "war is bad and total, unrestricted warfare is God-awful" from the colony gassings, colony drops and idealists on both sides getting used and abused by their respective governments in 0079.