But it does not do the 'return to Piraeus' journey every day and it's a much slower ferry, hence a much longer journey. The Zante Ferry is indeed an option worth looking at, as it's a subsidized route, with extremely low fares. We don't know on which date you will be leaving Milos, but looking at for July, you won't have a problem getting to Piraeus. We were fortunate to have a window of opportunity on the day of our flight and, unlike you and your family, we needed to get to Athens airport for a flight back to the UK later that day. Exceptional circumstances though, as a severe storm had been sweeping across Greece and the ferries were badly disrupted.
However, when we stayed for a week on Milos in September 2018, we chose to fly from there to Athens airport. All the reasons given by previous contributors support your thinking, I think you've already convinced yourself that, in your situation, ferrying back to Piraeus from Milos will be the better option.