I think the problem is that they didn't do one or the other until too late on. Had they decided they were riding for Sepp from earlier on the proviso that "we let the road decide, and because he's in the red jersey he gets priority", then it probably wouldn't have been met with the derision it has.
Had they gone full on 'let them race, we've got the podium locked up, let them duke it out on the road', then while it might have upset certain vocal portions of the twitterverse (being stirred up by members of the Anglophone cycling media), whoever won the race would be clearly the best rider in the race.
As it is, however, they've kind of half-assed it, so it's just ended up exposing that at least Vingegaard, if not also Roglič could have passed Kuss easily if they hadn't had their wings clipped, while simultaneously delivering an unsatisfactorily tame racing conclusion. They tempted us with some fratricidal battles, only to swerve us Fingerpoke Of Doom style into a lame love-in.
It's quite remarkable really, the team has somehow managed to completely dominate the race, taking five mountain stages across the three riders and locking out the podium, and somehow come out of this with a scenario where everybody looks weak in some way. Kuss looks like a lame duck champion who could easily have been passed by his teammates; Vingegaard and Roglič look like poor team players who were neither loyal enough to support their teammate nor strong enough to take command, and the team management look weak either way because either they told the team to ride for Kuss and were too weak to control their riders on the road, or they told the team to fight it out on the road and then flip-flopped in the face of negative comments on social media.