I wonder....could Darkness based powers (from Destiny) have any effect against the mental effects of the anomalies? Cause Darkness-based powers DO have heavy ties to the mind, emotions, dreams and memories, and more.
Can you imagine if the Magical Girl-type anomalies (Queen of Hatred, King of Greed, Knight of Despair, Servant of Wrath) and their antagonist (Jester of Nihil) showed up in one of our cities? MORE LOOT FOR THE GUARDIANS! Jokes aside, the E.G.O equipment from the abnormalities could be very useful....provided the sanity eroding effects are mitigated/nullified....
I read the wiki for Darkness and I still don't get it in general, but any mental protection that interacts with the "Result" of anomaly abilities should work to an extent, especially conceptual ones.
work despite not being able to interact, observe or manipulate the "process" in which it happens.
If we had M Corp's singularity, Moonlight Stones, we wouldn't have to worry about that since high quality Moonlight Stones negate mental damages altogether, even trauma from natural processes.
But since we're probably not so lucky, yeah, Magecraft can also help a bit if the technique stabilizes the person rather than trying to interact with the E.G.O.'s effects.
We can also try getting Solomon and our other casters to change the extraction method to apply a concept of absolute obedience or protectorship to the E.G.O. being made.
E.G.O. is essentially an extra dimensional higher being that can resist all laws and logic trying to analyze it, turned into equipment. Imagine looking into the mirror / another universe and the reflection beyond is just you, you but powerful, living as an existence that may had existed before time itself and interacted with every possibility in the multiverse, past present and future.
Which you call upon and turn it into an equipment, that's why E.G.O corrodes you and the reason why you can't just use the full power of the anomaly it is from, you essentially "wear" or "wield" the transformed body of a divine reflection, it actively fights for control, it gets worse depending on the Risk Level it is at, and so does the power it offers.
I'd suggest making some sort of smithing addition or creation contract with E.G.O being made from appropriate anomalies, ones that don't resonate with ideas of rebellion, like Knight of Despair.
This will prpbably turn them from Entities you bargain power with, into protectors, allowing you to access their full might in exchange for them being more active or trying to "protect" you in their own ways, so basically, Knight of Despair is prime candidate.
Imagine having true ALEPH agents, they may not be be able to break apart planets like super weapons, but they can wash technologically advanced worlds with destruction by their lonesome.
In comparison, the Heavenly Bull that Enkidu and Gilgamesh fought is around lower to middle level ALEPH in terms of sheer might, higher level ALEPHS like the Green Midnight can spam Black type lasers that liquify mountain ranges in an instant. You'll need power from the Gods to handle them safely, except for two anomalies.
I doubt we'd be let own an anomaly literally called Apocalypse Bird, so Twilight E.G.O is probably out of our reach, well at least Queen of Hatred's E.G.O can deal all 4 damage types at once like Twilight does.
Even without all of that, it's still possible for us to have very strong armies with E.G.O, WAW and ALEPH E.G.O seem to give the about same power as a HE anomaly, while the Astartes with their 45 times peak human strength and Bolters are only ZAYIN.
WAWs can take on an army of TETHs, scale that down to ZAYIN and HE and we have ourselves a good way to eliminate Battle barges from within and take on literal armies. It won't work against head-on confrontations against 40k ships, but it's still a significant advantage to have fighters able to take on Space Marines, Orks or Eldar infantry by the thousands solo (unless the opposition has strong support tech stuff to close the gap, or high level Psykers)
Edit: to clarify again, basically you're wearing/wielding a conscious existence, immune to most of the effects of reality but still responds to your Willpower and your thoughts, making it easier to wield if you're compatible in mind, but increasing the chance it takes over you, so if we have a way to make them indirectly obedient or imbued with conceptual level bindings, we can make them safer to use.
Of course, dealing with the mental corrosion directly also works, so long as you don't try changing anything about the process (of how it corrodes you, it will fail) without another E.G.O specialized for that purpose.