That's an interesting perspective, but perhaps I'm not cynical enough to think this really was a ploy? I think Apple could live without the brand tarnish from the Maps app (mostly, the errors in the data). It's becoming a running joke against the platform and a bit of a PR nightmare as park and police officials warn people not to depend on it. They also spent billions to acquire two mapping companies and developing the new Maps app. They probably didn't plan on a third party app coming in and plunking theirs down.
I just think they miscalculated. Mobile devices are becoming small glass windows to cloud services, most of which crunch large data sets to get you quick, meaningful and accurate answers. With Maps and Siri, I think Apple has showed that they don't yet have the competency here that they've enjoyed with hardware and interface. They'll get better, but I'd argue the game has moved to play more to Google's advantage.
But as you pointed out, as a third party app, Google Maps isn't a total solution (iOS has no true equivalent to Android's intents system). Tapping on an address in Mail or Siri will still open up Apple Maps. An SDK has also been released though, for those developers who'd like to integrate Google Maps in their iOS apps [1].
Users are the ones who really win. Now you've got two major companies competing for a great maps app on iOS. I suppose any win for users of iOS is a win of some kind for Apple too.
[1]
http://googlegeodevelopers.blogspot.com/2012/12/a-new-way-to-add-google-maps-to-your.html