The GTI uprising in Silent threats has some fascist vibes but the fact that you go from total war to scientific cooperation to actively protecting Vasudan civilian convoys(in Exodus) without so much as a single racist remark from anyone involved makes it pretty difficult to claim the GTA as a whole was fascist. I mean, both governments sign a cease-fire treaty alarmingly fast after the Shivans show up.
It's possible that the T-V war wasn't some 14 year total war of attrition where both sides were ready to cut each other's throats but closer to a feudal war where you have small flashes of action every few years but are still in a "state of war" for much longer. The war never ended because it wasn't THAT costly and because both sides thought they could profit from it.
The Harbinger exists because it works well as a threat. And it's not a planetcracker, it's a citybuster at best. A bit of strategic orbital bombardment is very different from outright genocide. We also know that some form of ground-to-space defences exist so that would give it a military use as well.
That and the almost total lack of any pro-human rhetoric or propaganda. During the T-V war all of your briefings and in-mission orders are very detached and professional, not what you'd expect from a fascist military. People don't really start getting emotional until the Shivans and the Lucifer show up.
As for the failure debriefings not all of them even blame you. Sometimes you fail, it's understandable, but you still can't proceed because that failure basically means losing the war. As for AWOL debriefings, yeah, that's generally what happens when you desert. All modern militaries treat desertion pretty damn harshly, fear is no excuse. This is doubly true when you're defending a capital ship with 10000 people on board. Even if the situation looks bleak you have a sworn duty to protect those people. Whether or not you can survive and/or accomplish your mission is not a moral problem, it's a tactical one. And therefore it's on your CO to make that choice, not you.