I am currently working on a cross-platform data exchange application. All flavors of the client talk to a common backend service which requires a one time payment or subscription fees (not decided yet) to be used after a trial period. The trial period is managed server side.
The payment processing would be implemented on the applications website in order to have a single point of account management and billing. Would this somehow violate Apple’s crazy “everything must be purchased through us” policy?
If your iOS tool is only the client for a webservice, I think you should be fine. I base this on the fact, that applications such as dropbox do the exact same thing.
If you get rejected because of this, apple might ask you to provide a possibility for your clients to pay the subscription through the app store for the same price you offer on your website. This will make you loose 30% of your revenue for each customer who does the transaction via app store.
We have asked apple about similar things, and all they do is send a short reply pointing to their terms of services etc.