Well, the same issue presented itself with Passbook and airline tickets, for example. I regularly fly Southwest and Alaska, and Southwest
still doesn't have Passbook integration. Passbook was fantastic when I was flying American and Delta, but it just isn't great enough to get me to switch airlines.
When (not if) this happens with HealthKit/Health, it'll be slightly disappointing to see these kinds of integrations from behind a glass window. At least some aspects of HealthKit are already being integrated with major fitness companies (namely, Nike), so not everyone will miss the boat entirely.