Something that really caught me when playing the original Freespace games was that it felt right to kill for the GTA. You are put into a pilot's seat, given strict military orders, and are told these are you enemies: go kill them. The Terran-Vasudan War doesn't have any meaningful reason other than a conflict over hegemony of resources. Why not simply explore more systems and expand away from each other? Why not trade? Because allowing your rivals to live means giving up absolute power. The game does a great job of having motives fall in line with that of a soldier under a fascist regime. The minimalism and emphasis on military procedures all build this feeling that it's ok to go and kill for the sake of resources.
We do not know nearly enough about the internal structure and politics of the GTVA to tell whether or not they're fascist. The games offer only a very limited perspective on life in the GTVA (that of a combat pilot on deployment in an active war zone); Any military will, by its very nature, seem fascist when compared to civilian life (That is not to say that soldiers are fascists, far from it; life in the military just is very much oriented towards working together for the greater good while under strict authority).
As a thought experiment, I once argued that a soldier from a liberal democracy has greater moral responsibilities than those of an oppressive regime. If you refuse to follow orders in an oppressive regime, not only are you likely to be put up against a wall and shot but likely your family too. If you refuse to follow orders in a liberal democracy, you are likely to be reprimanded and court martialed, with likely prison time, but it's unlikely you will ever be executed for it. Thus, a soldier from a liberal democracy, because he is less likely to be subject to unreasonable punishment, ought to exercise his duty to morals, rejecting orders that would constitute crimes against humanity.
A soldier serving under an oppressive regime certainly has a better excuse to make moral compromises for the sake of survival, but I would argue that both have the same duty to refuse immoral orders (I dunno, I'm german; During basic training, I was taught that it is our duty as german soldiers, as "citizens in uniform", to look out for and actively refuse to follow orders that cannot be reconciled with the values of our society).
While I don't believe any of the mission failures outright has the player be put up against the wall for a firing squad, you are treated rather harshly for failures. If you retreat before the mission is completed, no matter how absurd or seeming impossible a situation is, you are likely given a mission debriefing where you are court martialed or stripped of your rank. We don't punish soldiers for fearing for their lives, surrendering, or fleeing when the situation is bleak. The states that punish their soldiers under such conditions are typically authoritarian states, like Nazi Germany's policy of no retreat or Imperial Japan's expectation that their soldiers die before surrendering. As a pilot of the GTA, you aren't allowed to break orders. You retreat when Command deem it necessary.
"We" absolutely do. Desertion is a fairly serious crime, cowardice in the face of the enemy a pretty serious misstep in most militaries. This has nothing to do with how authoritarian a state is; It's a violation of the oath you swore when you decided to become a soldier, it jeopardizes the people next to you, and cannot be tolerated.
So I did post this in the Blue Planet forum for a reason. In Blue Planet, the GTVA is in fact seemingly very fascist in nature, especially when compared to the Ubuntu government. The UEF honor the lives of their fallen enemies, value the lives of its citizenry and soldiers, and refuse actions that it deem foul. When you fly with the Fedayeen, you are acknowledged to be in a unit that's not quite alleged to be part of the federation, even possibly disapproved by many of the elders and kept back until the situation became truly dire. The GTVA's equivalent, the SOC, are kept secret for purposes of information blackout, but they are acknowledged as being part of the GTVA are readily a part of the military service.
Did the GTVA become more militant because of the Shivans? Probably yes, but they were already a fascist society beforehand.
Again, we do not know enough about civilian life in the GTVA or the GTA before it to make that statement.
IMHO, the harsher side of the GT(V)A has two points of origin: One, the GTA is an umbrella organization for a far-flung colonization effort. We do not know how much (if any) terraforming the GTA has been doing (although we do posit that in the BP universe, they didn't do a whole lot; Mars' terraforming process was effectively stalled when extrasolar colonies became a thing), but we can safely assume that life on these new colonies isn't going to be particularly easy, especially after the events of FS1 and the loss of the Sol system.
Two, the shivans, obviously. After FS2, it is clear that the threat of the Shivans is much larger than previously assumed; they are, from the perspective of the GTVA, weakly god-like. Combined with the research into Nagari phenomena in BP, the GTVA is faced with an impossible mission: Ensure human (and vasudan) survival in a universe that contains agencies like the shivans and vishnans, agencies that are practically omnisicient, highly inscrutable, and which seemingly do not particularly care about human and vasudan survival.
In BP, we have posited a few things that the GTVA might have done in reaction to this, some secret, some not (Here's a small hint: The Anemoi class is vastly
overengineered for its current role). We have not, to the best of my knowledge anyway, talked about what life in the GTVA is like for the average colonist.