As anyone who played AoA through can attest, the strength of the beams doesn't matter.
The problem is, that the Raynor as so many of them, which makes disarming them in time to save your caps hard (at least if you sit in a Pegasus and try to disarm the Orestes, to save the Karuna in the last mission....).
I'm replaying the mod again but does saving the karuna really do anything ? (other than give you a nice tingly feeling
)
See, I tried that, but the sheer number of the Orestes' beam cannons make it impossible. However, I just started playing around with a VP extractor and modifying table values for weapons.tbl. I recommend setting the Balor's weapon damage to 10,000 and it's mass to 1,000,000. Next, shoot your Balor at the Orestes and watch it fly backwards right before exploding into a huge ball of flame!

As for who will win this war, it would obviously be the GTVA in a truthful mod, but seeing as you play this mod on the side of the United Earth, the UE forces will emerge victorious. I maintain that the GTVA's use of beam weaponry coupled with the fact that while Sol was separated from the GTVA, they let the Eastern religious teachers take over the world and brainwash everyone with their wimpy Zen ways. The GTVA's desire for conquest of Sol would naturally result in their victory.
If the UE is going to win this war in a believable fashion, they will have to do two things:
1) Hijack some GTVA military hardware and reverse engineer beam cannons.
2) Kick out the Zen teachers and stop being pansies.
3a) Pray to God that a friendly GTVBs Archangel Mk. 2 with a friendly IFF code jumps into the Sol system of Blue Planet's continuity from another FS2 continuity and volunteers to fight for the UE forces.
OR
3b) An Earth Alliance fleet from the Inferno continuity ends up in the Sol system of the Blue Planet continuity due to an anomaly in the Inferno continuity's Sol gate and volunteers to fight for Sol and kicks out the wimpy Zen teachers. (Kind of like how the BP:AoA GTVA ended up in an alternate Sol when they flew through their own Sol gate in BP: AoA, right?)