Only offer sign-in in the app (with no option to purchase / become a paying member). Netflix, Dropbox, Spotify, etc all do this, it's basically industry standard. Boom, done.
I would have expected this blog post 2 years ago; the fact that you were blindsided by this really doesn't give me a lot of confidence in your company. Anyone who's developed for iOS would have been able to tell you on day one that you're in serious gray-bordering-on-black territory with regards to IAP policy. Yeah, it sucks, and you can't really do anything about it. So suck it up and go with what everyone else is doing. Because so far, you've definitely lost me as a customer.
I'm an iPhone owner and I know that 1)you have no qualm about charging me more for the same service (apple's 30% notwithstanding) 2)you don't know much about iOS development and 3)your dissatisfaction with the platform makes me doubt your commitment to it in the future, and with data backup, I NEED to be confident in my service's future as well as its support of my device.