Surely the easiest way is to differentiate the iApp from your other services and then charge more
From what I can tell, the issue here is that Apple is:
a) Mandating that any publisher who distributes a content-access app provide an in-app purchase mechanism, and
b) Mandating that any publisher who distributes a content-access app provide equal or cheaper pricing through the in-app purchase mechanism when compared to all other purchase options.
Apple are also mandating that they take a non-negotiable 3%0 of any fees charge through in-app purchasing.
Now, I see what Lewis and others are getting at - if you're a publisher offering a weekly publication and you've got an iApp, you now have to have an integrated purchase mechanism in the iApp on which you make 70% of what you make through your own mechanism on your website. So even if this 30% overhead is higher than the equivalent overhead from any other platform provider, you can't adjust pricing accordingly.
The counter-argument is, obviously, that publishers offering their own platform will have costs that eat into the 100% of the money they get. But those costs probably aren't of the order of 30%, and those costs have other benefits such as getting more raw data on their customer base, etc.
Which has me thinking that the easiest way around this, for publishers, is to differentiate between their web-based subscription content and their iApp subscription content. Make the iApp a bit fancier, maybe have a couple of functions that you can't get through the web-based service...and bump the price by 30%. As an alternative, offer a free iApp that's just a skinned browser conveniently optimised to load the web-based version.
Now of course, the iStore Guardians will be vigilant against any such brazen attempts to Steal Their Rightful 30% Cut From Them....but, well...it's worth a try, right? Especially if the worst-case scenario is that you junk your free iApp and just offer a subscription-interface mobile page that's 30% cheaper than the paid iApp version. I mean, Apple will like it as they can even crow that there's an iOS-exclusive app from $PUBLISHer - they'll just quietly fail to mention that it costs you more than a similar method to access similar content through a mobile web interface...