Not sure. It may be unfair but throughout the race the situation is constantly changing, even if only incrementally. They used the 3k marker for Yates crash despite whether people were making time up. Same courtesy to the riders that crashed seems reasonable.
If it were my call, I'd take the times at the km marker prior to the crash.
How far did Froome actually run? Either way, I reckon he deserves the red numbers for that alone.