Well it's most a matter of Apple sherlocking features vs. shutting down because they want complete control over the user interaction model. As with most acquisitions, unless the team will continue to work on that app (and based on Sunrise, etc. even if they did), the existing version of Workflow will probably languish and the team's output probably won't surface to actual users for another couple of years.

It's mainly the idea that Apple doesn't want anybody else dictating how iOS should be used.