Spanish doctor Eufemiano Fuentes, the central figure in the trial, was given a one-year prison term for endangering public health on Tuesday.
The case attracted international attention because of the high-profile of some of his clients in Spain and beyond and his claim early in the trial that he treated a host of athletes in sports other than cycling.
However, the judge prompted widespread disbelief and condemnation when she also ordered the evidence, including code-named bags of blood, to be destroyed, rejecting a request for access from anti-doping authorities and dashing hopes that others involved in illegal activity could be identified.
She justified her decision by saying that evidence collected in a criminal investigation could not then be used in an administrative process such as a doping probe by a sporting body as it would infringe the rights of those implicated.
Spain's anti-doping agency (AEA) has said it will appeal, raising the prospect of the case, which has already lasted more than seven years since the initial police raids, dragging on towards September when the decision on the 2020 Games is due.
"The bid will be affected by both the good and the bad but we cannot be made responsible now for Operation Puerto," Blanco, who is also the president of Spain's Olympic Committee (COE), said in an interview with As sports daily published on Friday.
"We cannot correct the past but we can the future and that is our concrete commitment, nobody can doubt that," he added.
"The problem is that Operation Puerto has been a mistake and a disaster for Spanish sport from the start.
"The legal process has a timescale that is not the same as that in sport, where you have to decide things immediately.
"Now there will be appeals and the case will continue to drag on. It has been seven years already and that's a whole career for many athletes."
The World Anti-Doping Agency (WADA) also voiced its disappointment with the judge's decision to destroy the evidence and said it is considering an appeal.
WADA, the AEA, the Spanish cycling federation (RFEC), the International Cycling Union (UCI) and the Italian Olympic Committee (CONI) were all represented in the three-month trial in Madrid.
Fuentes, who denied doping, said in his opening testimony that he had clients in cycling but also in sports including soccer, tennis, athletics and boxing.
He offered to name them in court but the judge ruled that would have infringed the rights of those implicated.
"The verdict does not help the country's image," secretary of state for sport Miguel Cardenal told As on Friday.
"We will continue to devote all our efforts to find out these names and we will continue to explain that the outcome of a trial is one thing and another is our commitment as a nation," he added.
"They need to see that we are in the same boat in the fight against doping and that we feel the same frustration and the same disappointment."
Spanish tennis player Rafa Nadal, the world number five, added his voice to the criticism of the verdict on Friday, saying "the only people who benefited were the cheats".
"With something that damages the image of sport so severely, the ones who are affected are us the Spanish athletes and sport in general," he told a promotional event in Madrid.
"I think the best thing that could happen is that we stop talking about the issue."
Madrid is competing with Istanbul and Tokyo for the 2020 Games and International Olympic Committee (IOC) members are due to vote on the bids at a meeting in Buenos Aires in September. (Reporting by Iain Rogers, editing by Martyn Herman)