The Shakopee school board accepted Superintendent Rod Thompson’s resignation Monday night in front of a room full of people who had worked to unseat him.

Thompson was not present as parents and about 50 community members filled the boardroom during a public comment period at the special meeting.

“We are disappointed, frustrated and angry beyond belief,” Timothy Johnson said. “We have to look to the future.”

The board approved a separation agreement to pay $50,000 to Thompson, whose resignation is effective June 30.

“This allows us to get back on with the business of education,” said school board chairman Scott Swanson.

Community members in the Facebook group, Concerned Citizens of Shakopee, in collaboration with the local newspaper, Shakopee Valley News, launched an inquiry into Thompson that led to a police investigation and a search warrant issued on Thompson’s property on June 8.

The investigation uncovered a history of Thompson misusing his district credit card. According to the search warrant affidavit, Thompson made more than $3,500 in personal purchases, including a TV and a trip to Nashville. He later reimbursed the district for the charges.

Andrea Grugal said parents think the board should have investigated Thompson, rather than the community. Her husband, Gene Grugal, along with others, notified police of Thompson’s credit card abuse after filing data requests with the district.

“There were quite a number of rumors that there was a misuse of funds,” Grugal said. “Once I saw the data, it was laughable.”

Concerned parents and others began investigating Thompson, who was hired in 2011, shortly after the superintendent notified staff in March of a $4.5 million budget shortfall. In an e-mail to staff, Thompson said the shortfall arose from human error in budgeting and staff adjustments would be needed.

Mike Burlager, former finance director of the district, informed officials of the error in December and soon after announced his retirement. Burlager said that Thompson was the only one of 104 district employees who did not respond to requests for receipts, according to the search warrant affidavit.

In a Star Tribune data request of Thompson’s previous e-mails to district staff, Thompson called the error a sad and difficult situation.

“Many of the ‘human errors’ are the types of mistakes that a first year business manager would have caught and not made,” he said in an e-mail to Swanson and board member Reggie Bowerman in October. “Something has gone really wrong in the world.”

In an April community meeting, the board defended Thompson and the district’s actions.

On Monday, however, Bowerman stressed the need for swift action on Thompson.

“We are not hanging this topic over the heads of the district, community and staff as well,” Bowerman said.

Swanson read a statement that said pursuing any other option for Thompson’s ouster could cost the district $150,000 or more.

“In light of the current issues facing the school district, the school board feel that a change in leadership is warranted,” Swanson said in a statement.