Don't hard-link to a third party service. Abstract everything through your own site that you have 100% control over, so you can swap out the underlying services whenever you want.
I guess I don't understand the alternative. Go out of business?
It takes a lot of effort to build out your own store and get it right, this is no small task, which is why the 30% fee charged by these stores is not necessarily the biggest obstacle.
These intermediaries add considerable risk.
Edit: Sorry I know those were just two examples - I'm not trying to refute your point
For example, you can bang together your own store with Magento, Spree, or any number of other ecommerce store kits and pick one or more back-ends without a whole lot of sweat. This presumes you know a thing or two about web development and security, which is not necesarily a given for any group of developers. If you do know that, the difference between Stripe or PayPal is a few lines of configuration and API keys, if that.
[1] http://christiantietze.de/books/make-money-outside-mac-app-s... #noaffiliation