Thompson was found by an independent investigator to have committed one act of gender discrimination, three acts of marital status discrimination, three acts of family care/medical leave/disability discrimination and four acts each of interference and retalliation against six women who worked for the district.
Thompson's last official day will be Jan. 16, 2014. District Spokesman Trent Allen says the district saves money by allowing Thompson to resign.
"If you were to go for a termination with cause, you then have to produce a statement of charges," Allen said. "The superintendent would then get some time to review those charges, get some time to respond to those charges, has a right to a hearing before the board. That could easily be a 60-day or more process, at which time the superintendent would still be on paid administrative leave."
The decision by the school board did not sit well with many of the complainants, including retired prinicipal Christine Ohlinger.
"We understand the reason for the decision, but it doesn't make it right," Ohlinger said. "And we talk about integrity and the lack of integrity and making the decisions based on financial reasons rather than what's morally and ethically correct."
Twelve women filed complaints with the California Department of Fair Employment and Housing alleging discrimination and harassment against Thompson. The complaints of six women were sustained.
The district has received tort claims from the women totaling $17 million.
Thompson has been on paid administrative leave since May.