I can't explain the decision to bench them anymore than anyone else, but this went all the way to the level of Bob Iger, who's now back as Disney's CEO, so it was not made with haste. I'm certain they consulted with PR & Public Affairs, and knew the likelihood of external media attention. As I've previously said, I agree that relationships between non-subordinate colleagues are private matters so long as they don't become workplace matters. Godwin acknowledged that their behavior (as it is currently known) did not violate any policies. Still, it sounds like this became a serious workplace distraction once the affair was brought to light which is itself an issue executives must deal with as well. Moreover, Holmes and Robach surely had to meet with HR, Godwin, and perhaps others at the company, all of which is time consuming and distracting if you're also preparing for and hosting a show the same day. There may also be more to the story that we don't know, and the decision to bench for a few days may have also been a "warning shot" to Robach and Holmes to mind their behavior.
All in all, many possibilities, but ABC is not the JV team and I'm willing to believe there was a fair rationale for the decision. They were not terminated. It would not surprise me to see them back on air on Monday.