Just put a little dose of super-high-tech mixed with handwavium in and they work just fine.

Whilst the GTVA ships ripped things appart with beams - very similar to the Covenant...
The Covenant had just a single ship that used beams (not counting plasma turrets that Cortana reconfigured), the others were armed with some lasers for point defense and plasma torpedoes.
Not sure about that book with the "stealth spartans" though...
Remember all the way back in FS1? Operation Thresher had the GTA lose over 300+ fighters and pilots, and yet that didn't effect fleet operations at all it seemed.
If that came in answer to me: I wasn't talking about the fighter losses affecting the operation. I was just saying that so many dead pilots can't be hidden from the general public for long. And once those death get public, they put a lie to the GTVAs argument that the UEF is completely pacifistic and thus helpless against the Shivans, showing that High Command either was lying or seriously mistaken. Either way not a good way to stay in power in a society that's barely holding together in the first place. And the only thing that kept them together for almost two decades was the promise of reuniting with Earth (which helped focus the population into a common goal, but alienated the Vasudans - no pun intended).