Some in the crowd ripped away bike racks in the area of Pennsylvania Avenue Plaza.
Boente was asked to resign on Friday and two sources familiar with the decision to dismiss him said it came from high levels of the Justice Department rather than directly from FBI Director Christopher Wray.
A California church had argued that putting a limit on crowd size violates constitutional guarantees of religious freedom.
The man had been caught by the trailer tire, pulled under and was eventually run over by the tire, authorities said.
"In many places it appears the violence is planned, organized and driven by anarchic and far-left extremist groups using Antifa-like tactics," Barr said.
"We have yet another innocent man being killed by a police officer," said Anzhane Laine in Washington, D.C.
The president's tweeted remarks are a stark contrast to how he has called on other world leaders to respond during times of civil unrest.
“Black men in this city feel like targets. I feel like I could be next. It’s that bad.”
"An individual inside the vehicle began firing gunshots at contract security officers for the Federal Protective Service of the Department of Homeland Security," FBI San Francisco said in a statement.
"The campaign needs to push back strong and quick," said a Democratic state senator, adding that she's confident it will.
The historic liftoff was originally scheduled to take place Wednesday at the Kennedy Space Center in Cape Canaveral, Florida.
While tiny viral particles might travel through the air, it's unclear whether they could make someone else sick.