Their thousands / millions (they don't have billions, but even if they did, it wouldn't matter). Their lives don't matter. They aren't your responsibility as they are from another realm, namely one controlled (or which should be controlled) by the demons. All of them for one of yours. That's the kind of math you need to use.
I'd have to dig for it, but it is at one point mentioned that the witch population is in the billions spread primarily across their realm and your realm. So yes, it's billions, and not just in their realm.
Edit: Here's one snip in support of this:
Honestly, it was always a bit hard for me to accept that the demons could kill half of that many in such a short time, but let's just assume Ba'al could coordinate billions of demons across the realm that made a coordinated strike we weren't shown.
A resource that's more trouble than it's worth is a resource best discarded. Ideally, yes, they should be kept under control. But if they're proving to be a threat, they should be removed, and they're under the demon's jurisdiction.
If that's your actually opinion, you shouldn't stop at half. Of course, you'd be potentially throwing away a resource of billions due to the actions of a handful.
As for the threat, that comes from Ophelia and the upper witch leadership. The rest of the witches are essentially oblivious to the other going ons and likely to fall in line with Seraphina. There's hints of some past evil done by the Witches against the Demons in some of the things Ba'al says, but that's mostly presented after the decision is made, sounds like it's long in the past, and still incredibly vague. You and your mates can't be expected to make decisions or agree to them based on such vagaries and it frankly sounds like the Ba'al wants revenge purely for emotional reasons rather than tactical or political.
Going along with the witches' plan naturalizes the
current threat effectively since the main witch leadership is replaced and Ophelia's influence neutralized. And you're far less likely to have resistance elements since you didn't murder half of them.
The actual value of a resistance group has been VASTLY exaggerated. You need to have some other significant power providing substantial aid for them to be more than a mild annoyance against something like a superpower which both the demon and terran realms are.
You think your enemies won't try to support resistance elements in the realms you control? With the type of math you're supporting earlier of "no one else matters", I guarantee you will have more enemies willing to support elements to undermine you either to distract you from coming after them or destabilize your rule.
As for the "generations to come" thing; the witches don't have that many people to begin with, and they're going to have even fewer after the purge. 4 of them 350 years from now aren't going to accomplish a damn thing. Anyone even suspected of harboring thoughts of sedition can be put to death, along with their family, friends, and their pet spidermonkeys. The demons don't care. In fact they want to straight up wipe them out. They'll either fall in line or simply be exterminated.
As I mentioned, canon lore is there are 3 billion witches. Even with half killed, they aren't going anywhere. That's more than the population of any country on Earth. Even if just 0.01% of the remaining approximately 1.5 billion resist you, that's 150,000.
How much resources are you going to have to spend on finding these resistance elements, especially since the witches themselves are going to be incredibly reluctant to turn their own in? Going to be tying up the demons with the policing, or send your own people? Remember we barely were able to gather a few thousand to send. You really think the demons are going to have the temperament or desire to seek them out vs more wholesale slaughter or telling you to deal with it?
The realms are connected at known points so it's not like a witch is going to be able to sneak a bomb onto a bus in Idaho, and I doubt the demons even have the equivalent. The most they could accomplish is domestic terrorism which won't do a thing. The witches don't have twitter or CNN. Without any type of media impact terrorists and "revolutionaries" lose like 99% of their effectiveness.
Remember I mentioned that witches have significant presence in both their realm
and yours. So now you're going to potentially be facing resistance elements in multiple realms, including your own which doesn't have demons to take the brunt of it. In terran realm, the witches definitely have technology. And witches literally have magic. I'd be very surprised if that doesn't include ways to communicate amongst them. And I'm sure your enemies will be taking note of any signs of weakness or internal turmoil that the resistance might expose.
If you had to choose between alienating a long term ally and power that CAN pose a threat to you, or culling a few uncooperative and antagonistic people that don't actually matter, you'd prefer to piss off the billion year old ruler of hell in the hopes that he won't hold a grudge? Really?
It's naive to think killing half the witches won't alienate other powerful factions. Even if they didn't care about the witches, other rulers will see how you treat them. Sure, some might be compelled to fall in line with the show of force, but only as much as they have to while secretly hoping or working to free themselves from your yoke. And it's not outside the realm of possibility that some will become motivated to form a mutual protection alliance
against you if they become convinced they need to in order to protect themselves from a similar genocide.
And as I said, Ba'al clearly has a soft spot for the daughters. It's incredibly unlikely he'd actively do things to harm them or their future realm, even if he passively withholds support for a long time. It's a calculated risk in my opinion for a potential long-term gain of both the demons and the witches being long-term allies, and possibly smoothing over relations with other future allies.
Plus, I doubt this will be the only time I'll have conflicting opinions of action with Ba'al, especially if we continue to ally with more factions that will have their own demands. You'll need to be able to tell them "no" eventually or at a minimum negotiate them down to a compromise unless you want the demons to be your
only ally, and the unnecessary genocide of billions seems like a good place to start.
Edit: I do want to emphasize that while I think picking the Witches was probably the smart move, the way that MC and his bond mates go about it is profoundly stupid by lying to Lucius and keeping him in the dark. Hence why my original post has a "what I would have instead done" section.