And any Chaos polity that doesn't survive will have all of their worlds conquered by the Orks, which will then produce more Orks and Ork ships without end for whatever Warlord managed to conquer the place. Orks have almost always been a quantity over quality race, but when they get quality they are fucking scary. While we won't necessarily be dealing with a unified Beast Waaagh, there's a strong chance that the Orks will be much closer to the Beast level as a race. The simple fact of the matter is that the Orks can replenish their forces and fleets at a far, far faster rate than we can, which is why we couldn't leave the three Ork Domains right next to us alone - they would have eventually overwhelmed us even at their current level just through attrition. Once we get the super Orks that are coming, that kind of problem is only going to be worse since we won't have as much of a tech advantage. The Chaos polities on the other hand are mostly limited by human growth rates, which means that even if one of them is strong enough to survive this (which likely won't be without losses) that they won't be something akin to a von Neumann war engine.
And it's not "working with heretics" to just notify them. All it is is notifying them, and they can take whatever actions they want based on the information. We don't have to do anything beyond that, nor should we.
@Durin - what are the expressed opinions of the other people in the meeting regarding the possibility of notifying Chaos?