So there's no way the Great Mothers are happily going along with Thrawn and the Empire in S2, right?
Their way of interacting with the force is entirely based on a communal bond with the Coven, unlike the individualism and parasitic strength in the likes of Sith and Inquisitors. Aside from that, their societal structure and tribalism just isn't compatible with the autocracy that Thrawn believes so strongly in. Everything about the Empire and its fear-based hierarchical structure is in conflict with the society of the Nightsisters.
But more importantly, the Coven is connected across planets and, apparently, galaxies, through something like a force-web. When one suffers, so does the rest of the Coven. When one requires power, they lend it from the Coven. So I think it's highly unlikely they're unaware of the massacre on Dathomir, and I think they also discovered the truth of its orchestration in the whispers of the dead. Or at least, they're about to discover the truth on Dathomir if they didn't already know.
Like, there are a lot of dead Stormtroopers onboard the Chimaera, all of which are probably intended to be resurrected through Nightsister magick. Combined with all the dead Nightsisters on Dathomir, they could definitely pose a threat to the Imperial remnants (and the NR, at that).
"When you face one Nightsister, you face all of us"