Repeat a lie long enough and it becomes the truth. But that's only half of the point anyway, whether it's true or not. There's a lot of inherent value in slaying Kabuto regardless of how it affects the zombies. He's a super warcriminal at this point and killing him does at the very least ensure he won't be producing any more zombies. The other positive effect is that all the zombies whose originals wouldn't have been hostile would turn friendly after Kabuto's control ended. This would leave only Madara a big nuisance (and any nasty, villainous zombie we might not have seen yet, if there are such).
Still, it's not like I wouldn't like to see a good battle. Kabuto's behavior does suggest he has a few aces up his sleeve. If keeping him alive allows him to use them, then why not.