From an admittedly brief look through the source, it looks like the zone module does two things:
1. Creates the "Zone" and "Gate" abstractions, and,
2. Monkeypatches Node to use Zones and Gates.
To make setTimeout work, the zone module monkeypatches global.setTimeout and replaces it with a version that uses Zones and Gates. Rather than do that, what you could do is not use Zones and Gates at all, and monkeypatch global.setTimeout and replace it with a version that uses Promises. And: there, Promises work with setTimeout. Just as easily as Zones and Gates do.
(Alternatively, what many Promise libraries do is offer ways to generate "promisified" versions of individual non-Promise functions and encourage you to call those instead, rather than monkeypatching globals.)
My objection to zone is just the new abstractions, Zones and Gates. They don't seem to offer much (anything?) over Promises, and they seem needlessly incompatible with them. Instead of the two-part module, where you introduce Zones and Gates and also monkeypatch everything to use them, you could just have a one-part module that monkeypatches everything to use Promises. It would be less code and it would interoperate with the existing JS ecosystem.
I don't have a particular love for the Promise abstraction: it's just that everyone is going to have to learn and work with Promises anyway (since they're in ES6, and already in V8), and there's no reason to invent a new abstraction for asynchronous try/catch when one already exists. There are lots of Promise-supporting libraries, and no Zone-and-Gate-supporting ones, save for zone itself. Why bother with the fork?