I wonder what would happen if a group of people decided to raise totally artificial complaints about a good (or even maybe even a sub-par) unit or ability to see if it would get nerfed. If done right I think a substantial nerf could be given to the Hoshiko or the Drone Host as a result of totally off-base complaints (see: Siege Frigates).
From my experience, most Real Time Strategy games begin with fairly unique units and balance asymmetrically. For example, one faction may have a very potent unit compared to the others, but it has a weaker unit that balances it. Ofttimes there will be wholly unique units that each faction has, but others lack.
Then comes the complaints. Faction A doesn't have an exact copy of Faction B's unit, this is unfair. So gradually units are tweaked from all factions so they are more or less mirror images, usually with slight differences in cost or hitpoints, although they retain their visual look to maintain the illusion that there is some difference between them. We've seen this a bit so far with this game, Drone Hosts were a cheap, early alternative for Advent seemingly, but they were upped in price to make them just like the others, just a tier higher. Illuminators were unique creatures, doing a strange damage type and later, but made Advent do something than the traditional boring build a ton of LRF's to win, but this was changed to make Illuminators just like the others, but stronger. I would not be surprised if the more unique Capital abilities (particularly Advents) were chewed into.
Malice is a strong, unique ability. But the Mothership is also a fairly easy unit to down in battle (the thing gets focus fired into oblivion with easy in many battles, even with proper support). It may need tweaking, but it should be done so with care.
88Alex88, Detonate Antimatter of the Radiance doesn't just deplete some antimatter, it also disables the abilities. But if you are truly worried about it, get a Revelation and just chain hit one of the Capitals with Revier. And if you want, you can use two low level Revelations to totally disable two high level Capitals and stop them dead (talk about balance, right?). Each faction has a way to disable enemy capitals, and you can get them right off the bat, rather than having to get a Level 6 and a Level 5 ship together (which alone are far, far more valuable).
Your test was a wonderful set piece, but in a real situation it is a pain with such effect, and is vulnerable to a slew of things. If you mess up, you get destroyed easily by a hoard of Kodiaks that all the micromanagement they take is to click on a target and watch them die.
And just for clarification "25% of that 10k, so they get 2.5k". That will not happen for the very simple reason of Shield Mitigation (test if you do not believe me). Due to the way Cleansing Brilliance works, it forces the shield mitigation up throughout the attack, generally resulting in the target taking far less than 2,000 damage (a high level capital can get by with under 1,000 damage from the hit). The trickle down is severely effected by this factor. So to do 2,500 damage, it's more likely that you'll have to get 10 ships in the beam, and stay in the beam, which nearly all decent players would just avoid by spreading out. And honestly, if a player clumps up their ships that tight when there is Malice and Cleansing Brilliance on the field and also do not try to disable either of the ships, they likely deserve the blast they're about to receive, I think. Spreading out is far easier, since the way Malice works the ships have to be in proximity, and remain in proximity for the damage to propagate correctly.
It's a power combination, but it's no exploit (as much so as Returning Armada or TEC economy, I would say) and can be countered. Your only worry is if your opponent abuses Guardians (try getting Guardians, Repulsion, then playing with the ability). But the Guardians are for elsewhere...
Right now, Malice and Illuminators scare me far more, since they require comparably little micromanagement and relies largely on expendable ships. The dps that a large group of properly managed Illuminators can put out during a Malice strike can be terrifyingly effective (they literally can surpass Brilliance in some instances, and since they aim at different targets who will not be maxing out their mitigation, more of the damage is received and propagates). That I think is more of an issue than Malice and Cleansing Brilliance.
Sins Forums
. I dont want to have to deal with numerous hacks and stuff online and mentioning what an exploit is has just made the game 10 times worse! Mods really need to plaster a mail on the front page about exploits and to make sure everyone knows not to broadcast them. This is only a suggestion from me and for the good of the game not to be akward 
Stardock Forums
It's the best thing about Advent. 