This is a case where I don't think anyone would complain if they decided to give the same time to all those affected by this crash.
Well, there are some things to consider.
First, the rule was made to protect GC riders from timeloss due to crashes caused by others, usually those preparing the sprint or mechanical issues, with not enough distance left to make up for lost time. Whether 3k or 5k, that is not the point of the rule. They needed to agree upon a distance, but the distance as such is not at the center of things. Furthermore, a crash happening at 3.4k caused by spectators, reflects badly upon the organization, since they should do a better job ensuring rider safety to begin with. Also, in this case there was no ulterior motive, like there was in Tour of California, where the crash happened further away, and they ended up giving the group that had
previously been dropped (Van Garderen even missed the right turn and went off-course) the same time because they were supposedly held up by the riders still on the ground.