If we take her prisoner Danzo is going to have an army of corpse puppets within, like, a week. Because Danzo gonna Danzo.
On the other hand, if we just kill her he'll still probably have an army of corpse puppets, and/or Orochimaru will and that's only marginally less bad.
On the third hand, taking her prisoner doesn't actually guarantee the development of a countermeasure depending on how cooperative she is- not even getting into the possibility that Danzo has her killed in custody before they get that far because Danzo gonna Danzo.
On the fourth hand, the corpse puppets are really just flatly inferior to the already existing zombie jutsu that's already out of the bag- Edo Tensei- albeit Danzo probably doesn't know how to do that one because if he did know he'd have totally done it because Danzo gonna Danzo.
... On the fifth hand, capturing her instead of killing her almost guarantees we'll have to fight her again later.
On the sixth hand, killing her also basically guarantees we'll have to fight her again later but as an ironic zombie.
Ultimately I think we capture her, hope for actual countermeasures, then try to get going, like, an anti-zombie task force or something because zombies are a serious fucking problem in this setting.
(Also start thinking about assassinating Danzo, to stop Danzo from Danzoing.)
[x] Take the woman prisoner. Hisana can't guarantee that the research wasn't already passed on, or that the woman is the sole inverter. Konoha needs to know how to counter these corpse puppets