Something we've over the course of the campaign is that Ubuntu doesn't seem to able to persist in a world with an enemy not amenable to diplomacy. Just look at the state of your comrades over the course of the campaign. They either break down because they can't reconcile the necessities of war with their philosophy (like Kassim), or they abandon their philosophy entirely (like Simms). Hell, it looks like even Calder's starting to see things from the GTVA's perspective, even if he'd never admit it.
The UEF military is weak, simply because Ubuntu doesn't place much importance on it. Hence why 3-4 GTVA battlegroups are kicking the crap out of it. The problem isn't that the UEF can't produce good warships, it's that Ubuntu means they don't really want to.
After the GTVA wins the war, chances are they'll adopt the UEF economic model, and they'll probably end up looking more like the Jovians as a result. The entire war is meant to throw Ubuntu to the wayside, and the GTVA's reasons for wanting to do that have become abundantly clear.
The UEF's peacefulness was a product of Sol's stability. The GTVA's concerns about it are largely unfounded, because it would not last long outside of Sol. This is because it
runs completely against human nature. Some aspects of Ubuntu might spread to the rest of the Alliance, but they wouldn't become a bunch of pacifists like the Earthers. I say this because no peaceful philosophy, no matter how appealing, has ever managed to spread throughout the world, or even
a single continent in real life, which makes the GTVA's worries about it spreading throughout
an entire galaxy pretty ridiculous. It looks even dumber when you consider their borderline-paranoia of the Shivans, which would almost certainly prevent them from becoming pacifistic (fear will usually overcome love and understanding).
Hell, even the UEF is not completely pacifist, with the exception of the Earthers (who are mocked by the Martians and the Jovians). As for people breaking down, that happens in any war. Even the real-life US Army's veterans have high rates of PTSD and suicide, and they have a somewhat violent culture.
Honestly, I think the GTVA's leaders are mainly just pissed off that someone else is controlling Sol, however they may try to justify their invasion.