James Mee, who is Jewish, claims his Christian superiors ordered him to remove anti-Semitic remarks made by Gibson from his report. He also claims they ostracized him and prevented him from getting promotions.
The department denies the charges.
Superior Court Judge Barbara Scheper expressed doubts about whether Mee can win the case, but ruled that he can proceed to trial next month.
Mee had been investigated as the potential source who leaked his initial report containing Gibson's anti-Semitic rant, but no evidence was found that he provided the details to celebrity website TMZ.
Mee remains a deputy, but he no longer patrols for drunken drivers in Malibu.
It was not yet known whether Gibson would be called as a witness.
A trial on Mee's allegations is scheduled to begin on Feb. 14.
The Associated Press contributed to this report.