If the kit is too fluid that it lacks counterplay, it makes sense to nerf it that way. If the kit is balanced in how fluid it is but the numbers seem to be too high, then nerfing it that way is wrong. I honestly don't play zoe and I don't know how balanced her kit is on her ultimate right now but that's how the balancing should go I think.
I find it a little funny how riot nerfed akali's q to make it not proc off her e yet they added a fluid part to her w, and now she's broken top lane :P. That's just a side note, but nerfing a champion's speed of doing the combo and adding counterplay to it is not an issue, in fact it's good to do at times, it's just when riot makes it too clunky that it becomes a little of an issue.