Many of the journals currently publishing these kind of Registered Reports only publish special issues, which might help with your concern about journals being given control over what work is done in a field, though it also limits how much of the literature can benefit from the new approach.

Another way of thinking about a journal's incentives is that, by moving the primary peer-review stage before a study has actually been conducted, you greatly expand the number of studies that a journal will interact with, which may provide a larger and more valuable role for entities like journals in world where actual publishing is a trivial matter.