Castile, a 32-year-old black man, was shot and killed by officer Jeronimo Yanez in a suburb of the Twin Cities of Minneapolis and St. Paul during a traffic stop.
Riley Jay Davis, of St. Paul, considered going to Pride after hearing that organizers had asked police to keep a low-profile, but said Friday he will definitely not be attending.
In a letter, the police chief - a former Grand Marshall of the Pride parade - voiced anger that LGBT cops would be excluded. There will be fewer police officers in uniform compared to a year ago, when Minneapolis police upped their patrol after the shooting at a gay nightclub in Orlando, organizers said.
Among the largest pride celebrations in the country, the Twin Cities festival now draws 350,000 people every year.
The criticism included a strong statement on Thursday from Minneapolis Police Chief Janee Harteau, the city's first openly gay chief, who expressed her unhappiness and said the decision was hurtful to many officers.
"For an organization that prides itself on being accepting and inclusive, the hypocrisy amazes me", he said.
"I just think anytime we can have a conversation and understand opposing views, we find out we have a lot more in common than we do different", Harteau said.More news: FIFA Confederations Cup: Portugal, Mexico through to semi-final
"I know historically, our minority communities have had struggles with police interactions; that is why we've worked so hard to build relationships that I still feel are both valued and respected. I look forward to seeing everyone out at the parade on Sunday", she said.
Organizers originally wanted limited participation in wake of the not guilty verdict of the shooting of Philando Castile. "Seeing those uniforms brings angst and tension and the feeling of unrest".
Chanting "no justice, no Pride", the protesters blocked the path of the parade, intersection by intersection.
The protesters who halted the parade shortly after it began were carrying signs with phrases including: "Black Lives Matter", "No KKKops at Pride!"
In a Friday statement posted on Facebook, Pride Executive Director Dot Belstler and the board of directors apologized "to the law enforcement community for neglecting to communicate and consider input for other possible alternatives prior to releasing the details of this decision".