Hi Peter,
Once we remove PNaCl, this does mean PNaCl applications will cease to function.
We're delaying removal slightly due to the temporary removal of SharedArrayBuffer and related delays with WebAssembly threads, but do expect removal to go forward once there's a threads migration path turned on in Chrome.
I'd be curious to learn more about your use case, and if it would be amenable to WebAssembly, and will email you off thread.
-BradN