I've had this happen to me as well, and I spoke to Riot Support about it:
"Zilean's Ult is not really considered a heal. It's more like doing a system restore in the Windows OS. I can see why you would ask though. His ult is very similar to heals but the mechanic is quite different." -Spine Splitter, Player Support Specialist
On pointing out that this amount "restored" is still prevented by Kindred ult even though it's not technically a heal, I got this response:
"You got a point, Summoner. Even though Zilean's ultimate is not considered as a heal, Kindred's ult still prevent's the champion being revived, gain HP.
Zilean is getting an update in the PBE right now so I believe you could post your opinions and suggestions on the PBE thread."
-jeProx, Player Support Specialist
But since that PBE change has already gone to the live servers, I don't know if posting on the PBE thread will change anything, so I'm trying my luck here. I've also got a video of that interaction happening:
https://www.youtube.com/watch?v=vmDKw7xCQEc