From what I can see, the wine with spinal fluid is for the exclusive use of officers. There's even a separate room for them.
My guess is that Yelena somehow co-opted Nicolo early on. From what Zeke says, even a minute amount of his CSF is enough, so perhaps a drop per bottle or even less. She could have had a flask of it in her possession when they put whatever plan they have concocted in motion.
I guess… Zeke will target the Eldian leadership, not the Eldian people. Perhaps he's trying to decapitate both countries so as to make the warring mentality stop. Or something along these lines. It's hard to tell with Isayama.
The problem is, if there isn't any antidote, they have to round up all the officers who drank the wine - including Nile Dawk, unfortunately - and confine them before Zeke decides to send the coordinate to Titanise them.