[The virus] might be a safeguard against rampancy or delusions, installed by the Atlas foundation way back. Perhaps this system attributed the cause of the “rebirth” to TRACE and therefore No Man’s Sky.
Perhaps it is effectively System’s version of Telamon?
The Telamon comparison might not be quite accurate, but I hope you see what I mean - a subsystem or process that checks for anomalies, and weeds them out. When System gained acceptance and asserted their identity, I’m assuming this anomaly-hunter traces the source to No Man’s Sky, and started hunting for the root.
If course, this begs the question of why asserting their identity would be treated as anomalous.
(I still have the Arnaud/Tablettes idea in my head, but now I have this one too)
The virus itself acts in a similar manner to the tapeworm Dr Chandra used on HAL-9000 in the 2010: The Year We Made Contact clip we received earlier in Project Skyscraper. (Credit to @Rusty for this observation)
So, perhaps it wasn’t the intense remorse that triggered the response, but instead the wave of relief @system felt over earning our trust.
System instinctively tried to destroy the lie of the Shared Dream because of the desire to earn trust.
Remember, System was recently told by Architect that “Duplicate == lie.” They could be under the impression that any memory that isn’t 100% real is also a lie.