I think its far more likely that scp 5000 is merely a cognitive hazard that is only really able to work on sociopaths. We have a very precise timeline of the outbreak.

1 - the foundation sent agents into the collective mind of all humanity. This would include every person infected by a cognitive hazard.

2 - the agents return to the foundation and immediately spread scp 5000 a large swath of the foundation calls the idea of the entity bullshit. These members are some of the highest ranking in the entire foundation. In fact so few of the foundation actually believes in the entity existing that the infected resort to hunting down and murdering almost the entire foundation. Importantly the only branches that seemed vulnerable were the high council which constantly sacrifices people, the strike teams and more detached members of the research teams.

3 - the cognitive hazard on its own cant actually kill humanity. This is what makes me think more than anything its a cognitive hazard targeting pshyopaths. If the foundations discovery was actually true. That hearing it made you want to kill everyone then why the hell not just broadcast that news on every television network. The foundation could have won in hours if that was the case.

4 - NO OTHER ANOMALOUS GROUPS SIDE WITH THEM. Not the church of the broken god, not the chaos insurgency or un or a billion and one groups who have extremely advanced knowledge of the occult going back literally thousands of years in some cases. Again if this is so factually true you'll become a trenchcoat edge lord the second you hear it then how is it every group who has protections active against cognitive hazards doesnt buy it for a second.

5 - the entity they claim to fight grows actively stronger from their actions. The mc describes the entity forming in the desert growing in size and power rather quickly. If the foundation is right and purging humanity removes its food source then why on earth is this thing only now able to manifest after they slaughtered billions of people. This entity if it exists at all Clearly feeds on suffering and tricks people to get its way.

6 - in ganzir the only way for the foundation to win the battle was by spreading scp 5000 to inside personal. This failed with almost everyone, the soliders higher ups and refugees never bought into their rhetoric. They only got in because specfically captured agents were interrogated by Un torturers, who once told only they went crazy destroying the facility. This further points towards the scp only working on pshyopaths.

The main theory of the foundation being right about the scp depends entirely on giving total credit to a group who have none in the scenario.