I've always found this a bit ironic of an argument since the demon path literally involves the death of billions.
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.
Yeah, they aren't directly your people, but the ultimate goal is to have an alliance or control over them. So indirectly they kind of are.
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.
I also think that it's pretty naive to think that the Demon path won't be dealing with underground witch resistance fighters for generations to come after you're responsible for the genocide of half their people. Not to mention that Seraphina's days are likely numbered, especially if/when it comes out she's magically bound to you. She's going to be facing constant coup and assassination attempts for a very long time for her role in allowing things to get to that point.
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.
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.
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.
Personally, I view the Demon path as the "short term gain, long term problem" path compared to the Witch path. Yeah, the demons are angry with you short term on the Witch path, but it's not like you've murdered half of them or left them under witch control. Ba'al clearly is fond of the daughters. He'll probably get over it eventually, and likely without directly causing problems for you in the meantime.
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?