What has to change the most is the attitude with which riders and DS-s approach those first week flat stage finales. There's far too much nervousness in the Tour peloton, too much fear of stupid small time losses, which often leads to losing the race altogether in some stupid and completely avoidable crashes. Too often this is accepted as inevitability and most of the attention turned to ASO-s road planning even if out of all the crashes so far, only one can be attributed to roads being too twisty and narrow for a sprint stage.
Riders and specially DS-s need to take a hard look at themselves, and find ways to cut down this nervousness. Specially the GC teams have very little to gain and everything to lose in those flat stages first weeks. Maybe the 10k rule would help a bit, as the sprint leadouts and fight for the position are usually yet to get going at that point. But more important is to change the attitudes like that of a GC team having to fight for position with sprint teams in the lead up to the neutralisation line in order to keep their leaders safe.
Some changes in the rules may help, but I don't believe that those alone can do enough. The teams need to sit down and come to some kind of working agreement on how to approach those flat stages, if only for the Tour, as other races aren't usually this kind of demolition derby. They have the responsibility to do so for their own riders and the sport of cycling as well.
Crashes have always been part of this sport, but when the biggest race of the year turns regularly into a demolition derby due to excessive nervousness of the peloton, then that peloton has no excuse of doing nothing about that nervousness. Concentrating only on road planning issues is no solution.