Often things win not through fair competition. For example, WebSQL "won" on mobile because WebKit won on mobile, and WebKit happened to have WebSQL. If WebKit had had, say, the Audio Data API (which it did not), then the Audio Data API would have "won". Neither of those APIs won or would have won on its own merits, but because it was backed by the 800 pound gorilla in the space. (I chose Audio Data as an example because it is not in the same space as WebSQL, i.e. not competing with it, and was a nice API, that failed).

And the problem is that PNaCl will fragment the web, and already has. That's a serious problem - for everyone but Google.

SPDY initially began inside Google. But rather quickly it got enthusiastic interest from multiple outside parties, and a standardization process began. We can see the (successful) end of that process now. Yes, it's true that many standards begin that way.

PNaCl also began inside Google. Discussions regarding it, and the PPAPI on which it depends, were a combination of opposition (e.g. because PPAPI duplicates existing web APIs, and because it's a plugin API, which browsers are trying to move away from) to ignoring. Google continued to work on it, enabled it on the Chrome Web Store, and despite any change in the response of the community over a period of years, enabled it for web content. Over a year has passed since then, and it seems clear that (1) no browser outside Google thinks PNaCl is a good idea, and (2) no significant interest has been shown from non-browser vendors either (Google itself is the main user of PNaCl).

Also, to make things even worse, during all that time, PNaCl has not been brought to any standards body.

Another large difference is that, in practice, SPDY didn't pose a compatibility threat to the web. It has clear fallbacks so that content still works without browser support for it. And while it is possible bugs could still cause breakage, it didn't happen in practice. So moving forward somewhat quickly with SPDY was still arguably a responsible thing to do.

Whereas, PNaCl is already showing fragmentation problems, with several Google properties using PNaCl and consequently only working in Chrome.

There is therefore every reason for Google to disable PNaCl, because it is nonstandard and bad for the web to keep it on. Unless Google simply does not care about standardization here.