Before yesterday's stage race director Christian Prudhomme condemned the incident and asked for fans to respect the riders, but the Tour organisation also came under criticism.
But he was caught by Fraile before the summit, and the Astana rider easily held off Stuyven and Julian Alaphilippe in the final 1.2km to secure victory.
For a long time, it looked as if Thomas, a two-time Olympic gold medallist in team pursuit, would relinquish his yellow jersey as Kruijswik opened up a commanding lead in the climb up Alpe d'Huez.
Sky are unpopular with parts of the cycling community in France, where their domination - winning five of the last six Tours - is reminiscent to that of disgraced Lance Armstrong's U.S. Postal team in the early 2000s.
2014 victor Vincenzo Nibali has abandoned the Tour, after fracturing a vertebrae in his back when he was brought down following a tangle with spectators near the top of the climb up Alpe d'Huez.
The Nibali incident occurred where the course narrowed and thick red smoke from spectators' flares reduced visibility and caused the Tour motorbikes to brake violently.
"When I attacked I was not sure I would be able to keep my advantage".
Jasper Stuyven led the chasing pack by one minute 40 seconds going into the final climb of the 188km stage.
Thomas is the current leader of the race, now 1:39 ahead of his own teammate and four-time Tour victor Chris Froome.
To muddy the waters further, Froome has not - yet - ridden like a man destined to win the Tour, looking panicked when left without teammates on stage one, and producing ineffectual attacks in the Alps rather than his usual searing accelerations. "I don't even know what happened myself".
Froome and Team Sky were booed on the podium at the start of the Tour in the Vendee.
Bardet crossed 14 seconds behind Thomas, Froome, and Dumoulin and his gap behind the yellow jersey holder fell to 3 minutes, 21 seconds, in fifth place overall.
Froome isn't super popular in Tour circles due to his previous doping scandal, but that doesn't mean he deserves to get pushed.
Stage 15 on Sunday from Millau to Carcassonne is another hilly leg before the race's second rest day on Monday.