"Apple CEO Steve Jobs supposedly responded to some emails sent his way saying that the in-app subscription policy was meant for 'publishing apps, not SaaS apps'....It’s certainly possible that even the App Store reviewers were confused by the rules at first and started rejecting some apps that should have been let through."

This explanation seems quite likely but I also think it's a case of Apple seeing how far they could push the envelope (like they did when they stopped allowing Flash based iOS apps).

If the public were relatively okay with it, then they may as well proceed and enjoy the extra profits. If however it means less people getting iOS devices and opting for Android/Windows devices then Apple are left with no choice but to retract from their strict stance.

A business is nothing if it doesn't have customers.