Following this train of thought simply leads to a further moral dilemma. If the concern is that Instapaper is bad because it bypasses the content providers income methodology then Readability is also bad because it does the exact same thing. The only difference is that Readability has created their own income methodology, of which a portion they feed back to the content providers (sometimes). At no point does either service require a content provider opt-in before the service's users are able to pull content from the providers.
I believe Instapaper has an opt-out function for content providers whereby Instapaper users are prevented from adding that content providers content to their Instapaper account. Does Readability have that opt-out capability as well? If not, Readability could very well be considered worse than Instapaper on a moral scale since Readability then becomes a form of blackmail: agree to accept payment for your content that we decide is just, otherwise we'll simply eliminate your existing payment method anyway.
I fail to see how any moral analysis of either service could conclude one is good and the other bad. They are both bad from the perspective of the average content provider. Half measures, and possibly blackmail, do not assuage the moral concern.