On Sunday, a protestor caused a minor crash that involved Spain's Javier Romo, who abandoned the race on Tuesday saying he was "not feeling very well, mentally or physically".
The 26-year-old Movistar rider had suffered "only bruises" during the fall and was able to complete the race on Sunday but quit with 80km to go on stage 16.
The team time trial in stage five was also disrupted when the Israel-Premier Tech team, owned by Israeli-Canadian businessman Sylvan Adams, were stopped on the road by a group of protesters holding Palestinian flags.
There have been calls from some quarters to suspend Israel-Premier Tech from the race, but Guillen said it is not for Vuelta organisers to take that decision.
"Yesterday, there was a match between Italy and Israel," the race director said, referring to Monday's Fifa World Cup qualifier between the sides.
"A football match was played, and a European Cup in which Israel participated has taken place.
"The participation of these teams is not prohibited because no international federation has done so, none. And there hasn't been any international body that has imposed sanctions requiring us, the world of sport, to act accordingly.
"From now on, what we want is for the race to continue because all the teams participating in La Vuelta have legitimacy."
The Israeli military launched a campaign in Gaza in response to the Hamas-led attack on southern Israel on 7 October 2023, in which about 1,200 people were killed and 251 others were taken hostage.
At least 64,605 people have been killed in Israeli attacks in Gaza since then, according to the territory's health ministry.
Bernal, riding for Ineos Grenadiers, secured the victory on stage 16 in three hours, 35 minutes and 10 seconds, finishing ahead of Spanish rider Mikel Landa.
France's Brieuc Rolland took third place, while British rider Finlay Pickering, 22, finished eighth.
Two-time Tour de France winner Jonas Vingegaard remains top of the general classification with Joao Almeida 48 seconds behind, while Great Britain's Tom Pidcock sits third.
Friday will feature another medium mountain stage stretching 143km from O Barco de Valdeorras to Ponferrada.