(iOS developer here.) As an iOS user I'm generally very happy with the various app restrictions, because they increase my control over the device and my confidence that apps aren't doing naughty things behind my back.
On the other hand, there clearly exist good product ideas* that need more privileges, long-lived background execution being one. There ought to be a way for a proven good actor to get blessed for special entitlements where they're critical to the product. (There's already at least one entitlement in this model: "Hotspot Helper".)
On a technical front, Apple's positioning the iPad as a laptop replacement; well, the users who are going to buy into that are going to be using authoring, productivity, and communications software that they'll want to be flexible and responsive. That might mean -- horrors -- the occasional helper daemon...
*I don't actually know if RescueTime is in this bucket; I'd never heard of it before this article.