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I know that selling things without going through App Store In-App Purchases etc. is not allowed widely. Even apps like Dropbox historically had problems with it and even they use in-app purchases for Dropbox upgrades today.
If I'd develop an app that people donate charities using an online payment system (like Balanced or Stripe), would Apple still take my app down because I'm not going through in-app puchases?
I have here some App Store Review Guidelines, but you can't use in-app for donations. There are some points in the Apple In-App Purchase Policy covering some of your questions:
21. Charities and contributions
21.1 Apps that include the ability to make donations to recognized charitable organizations must be free
21.2 The collection of donations must be done via a web site in Safari or an SMS
Source: https://developer.apple.com/appstore/resources/approval/guidelines.html (late 2013)
I don't believe that limitation effects Apple Pay transactions, since it's not going through Apple's in-app purchase program. It also wouldn't be subject to Apple's 30% cut. Apple would get a portion of the transaction, but in the form of a fee charged to your credit processing merchant for the service of generating the secure Apple Pay transaction tokens.
The main problem with using Apple payment frameworks for donations is that Apple doesn't share user information. Non-profits need user information like name and address for tax purposes. But you can't collect this from Apple.
