While the bigger issue is that the Tour organizers have total egg on their face, once again, and this is looking like one of the worst Tour ever, hence their decision I think. But it brings up questions:
If Froome hadn't been in yellow, but DeGendt was before the day, would the ruling have stood?
If this had happened to DeGendt, Pauwels and Navarro, what would the organizers have done?
Bertjan Lindeman finished 2:52 back of DeGendt, but was ahead of the crash. What if this would have happened to him instead of Porte?
Pierre Roland, Geraint Thomas and Ilnur Zakarin were about a minute behind the Quintana group. What if this had happened to them?
I agree with whomever said it would have been a better story if they would have apologized for the chaos, but let the results stand (and waive punishing Froome for running without the bike). Having Froome take back yellow would have added drama. As is, he's going to easily win by over 5 minutes unless something happens.