I think there is a bit of a difference with leadouts. Lead-out men cutting their effort is expected by everyone involved in the sprint. What Jungels did was completely unpredictable. It was reckless and directly injured another rider. Perhaps throwing him out is too harsh, but he should get some kind of yellow card. And if he does it again, then DSQ.
In XC skiing, skiers are given yellow cards for violations, and these are displayed next to their names in the results sheet so the jury instantly know who is on a warning and who isn't. These can be for endangering people, for recklessness, but more often than not it's technique violations (using too much skate step in a classic technique race, for example). However, this would perhaps be a good idea in order that riders know when they're on thin ice, and also so that you can punish people outside of the current "relegation or DQ" kind of level. It could also apply to missing the time cut if they reprieve the autobus - they all get a yellow card, so they're thrown out of the race if they then commit a violation like a dangerous sprint or a swerve like Jungels today.
For a lot of riders, the penalties imposed are meaningless ("oh, you're giving me a 2 minute penalty and taking away 20 points in the points classification? I had 0 points after 15 stages and I'm 2 hours down on the GC, take what you want") and the example of the Renshaw DQ in 2010 comes up again - Renshaw headbutted another rider, then put a different rider into the barriers with a reckless swerve within about 150m of one another. If he's put to the back of the group, why should he care? He led his guy out and his guy won - so if he'd only done one of those things and been allowed to stay in the race, there is no punishment. And also if we'd
known Sagan was already under observation for an incident at an intermediate sprint earlier in the day, the DQ in Vittel would be a bit less controversial a decision, because people would have seen he was on a yellow card when his name came up in the results and therefore while they may still have disagreed whether the decisions merited a yellow, they'd understand the reasoning behind ejecting him instead of just relegating him as was the original punishment.
Having yellow cards that stay with you so can see you thrown out the race (or given a suspension if you rack up too many of them like in football or motorsport), if nothing else, might help at least make things a bit more transparent.