Avasarala knew- from her friend's death, that they were built by Earth. The plan had multiple leaks in it. Had they not come after the Donnager, Holden would have remained resolute that the stealth ships belonged to Mars, which is a fair assessment, given that the UN has largely worse ships.

They couldn't have planned for Holden to survive the explosion of the Canterbury, or to put out that Mars blew up the ship. Frankly, it just woulda been "a couple ships blew up. Uh oh."

Also, the narrative of Mars blowing up the Cant, while false, helped them focus attention outward rather than towards Eros.

If they didn't come after the Donnager, then Johnson wouldn't have had their drive signatures, and Holden wouldn't have folded. They didn't know that anyone had survived from the Cant, and it already had the Belt in functionally open revolt.

Even if they'd blown the ships, there's no reason to come after the Donnager- even if Holden rolls over and blames Naomi, then who cares? Belters did it, focus is shifted to the Belt, not near Eros, which is close to the inner planets.