Reviving a slightly old thread but clicking on the "direction" button in Google does indeed take me to the in-browser map instead of Google's external map or Apple's Map. There's also a link that says "Always open in the Google Map app" which doesn't seem to work at all. On 6.1.2.
I actually went to an Apple Store today and turns out that all the demo phones there 4, 4S, 5 also have the same problem not pulling up the native Maps app from Safari. Also, Hashbang Production (guys who developed MapsOpener) mentioned this problem to be on Google's end. You've tried on 6.1.1 and 6.1.2?