how did no rider have a disadvantage?
I've rewatched it, and the situation was quite undramatic - the other riders in the group hardly noticed what he did.
Relegating a sprinter is equivalent to disqualifying him.
Not really. If it's a stage race, you stay in the race. If it's a big one day race, you get loads of UCI points for being relegated to fifth after a five man group sprint. That's actually one of the reasons why many riders take big risks in sprints: it's not that bad for them if they get penalized. (Lanterne Rouge has shown that to perfection.)
Relegating MVDP in this scenario (a) would have made no sense, because his continued presence has already influenced the outcome of the race
The same in sprints. Sanctions can rarely restore a just outcome - their purpose is to make riders respect the rules.
and (b) would have been just as bad from MVDP's perspective since it would have booted him off the podium.
If you have a penalty that is less harsh than disqualification, there will often be situations where that penalty hits harder than in others. It's like in football when a player gets a red card after 1 minute of play and another player gets a red card with 1 minute remaining. The offences may be the same, but the consequence is far more severe in the first case. That's just how it is.
Even if Van der Poel missed the podium because of a time penalty or some other kind of sanction, I would still regard it as more proportionate than disqualification. As mentioned elsewhere, a yellow card would also be fine with me, although the current yellow card system seems too soft in my opinion. Two times jumping over pavements (within half a season or a whole season) should lead to a ban.