Killing the Manei domini is irrelevant. Why does everybody keep assuming that the Manei Domini have to somehow survive to win?
And why in gods name would the Manei Domini attack just one world in the first wave? They would hit everywhere at once, or as close to it as humanly possible. Once they're in the atmosphere, the game is done, any damage their troops do on the ground is pure gravy.
Look, biowarfare is terrifying. To counter it, you have to eliminate all possible chance of contact, as Galax demonstrates, that means you have to keep every manei domini from getting so much as a tiny canister into the atmosphere. The ENTIRE atmosphere. The blakists have demonstrated their ability to create bugs that can adapt and live within completely alien biospheres (on Galax, every lifeform on the planet was turned into a carrier for the plague). So you have to be able to police the entire planet from intrusion which you may (in fact, probably will) never see coming. How do you protect an entire planet from purely inertial objects maybe no bigger than a phonebook? These capsules don't need to be that big, and they certainly don't need to be made easy to detect.
And if you can't prevent infection (and you CAN'T), you now have to fight alien bugs genetically engineered to kill you before it spreads beyond your ability to control. And not those prissy targeted bugs the Society created. These things target everything, can live in everything, and it's not going to be a single disease, because that would be idiotic. You've got multiple bugs attacking from multiple vectors, and any one of which is enough to lose the game if you can't contain it.
And the fact is, you can't contain it, because odds are, by the time you realize you're under biological attack, it's already spread beyond your control to contain it. The contagious period and the symptomatic period are not the same thing. For example by the time the Combine realized what the curse of Galedon was, not only was Galedon already gone, but the contagion had already made it to An Ting, which went the same way.
So not only will the steps necessary to stop the attacks not save the targeted planets, the clans won't even realize what's happening until it's too late to to do anything about it.
The Clans will see the Manei Domini die, they will probably even get to kill large numbers of them. In fact the plagues will probably take years to run their course, but these are all cold comforts. The homeworlds will never threaten the inner sphere again.