K. William O'Connor, special counsel of the Merit Systems Protection Board, yesterday charged two Defense Department officials with discriminating against an employe because of his religion, in part by making "repeated anti-Semitic remarks" about him.

O'Connor's complaint charged that Dennis L. Zimmerman, a manager with the Defense Logistics Agency, and Michael Pouy, a subordinate, taunted agency employe Wallace H. Weiss with such slurs as "rich Jew," "resident Jew," "Christ killer" and "nail him to the cross."

The complaint said that when Weiss, a research analyst, complained about this treatment to his superiors, his performance rating was lowered and he was denied the training necessary for his job. The complaint said these actions were in reprisal for Weiss' complaints of religious harassment.

O'Connor's complaint alleged that Zimmerman made Weiss' work environment "offensive, hostile and intimidating on account of his religion." The continuing slurs caused Weiss to develop stress and anxiety-related disorders, according to the complaint.

Weiss was fired in August 1983, but a federal judge in Alexandria ordered him reinstated with back pay last November. In a civil suit brought by Weiss, U.S. District Court Judge Richard L. Williams ruled that top DLA officials were aware of the religious harassment of Weiss but refused to discipline the employes involved.

A DLA spokesman said that Zimmerman and Pouy would have no comment.Quail Refuge Planned ----- The government plans to spend $9 million to buy an Arizona ranch for use as a national wildlife refuge for the endangered masked bobwhite quail, Interior Secretary Donald P. Hodel said yesterday.

Critics have complained that the $9 million purchase price for the 21,258-acre ranch near Tucson is too high. The price also covers the ranch's grazing rights on more than 90,000 acres of state land.