A front office dispute ended with a show of unanimity yesterday as the San Diego Padres announced that Manager Dick Williams would be back for his fifth season in 1986.

Williams, upset by what he perceived as an attempt to oust him, had thought of quitting and accepting a buyout of the final year of his contract. But after a meeting with owner Joan Kroc and executives Ballard Smith and Jack McKeon, word was issued that Williams is staying. Officials blamed the weeklong upheaval on a series of what Smith described as "unfortunate miscommunications."

"We had a misunderstanding and I am sorry about it," Smith said.

Smith read a brief statement from Kroc, his mother-in-law. Kroc reaffirmed her confidence in Smith three days after publicly rebuking him and McKeon for what she saw as attempts to make Williams quit.

Smith also announced that third base coach Ozzie Virgil, a trusted Williams associate fired last month without Williams' consent or knowledge, would be rehired.

"There are some things about (Williams') management style that I don't like," said Smith. "There's probably some things about my management style that he doesn't like . . . we will both work on our communication skills."

Smith admitted concern that Williams' gruff managing style alienated players, many of whom anonymously told the media they were hoping he would leave.

"There'll be a player revolt if he comes back. It'll be chaos," one said. "I love playing for Dick, but when I get out of this game I'm gonna run over him with a car," said one.

Smith said he didn't think the players' alienation with Williams was irreversible or "to the point that he can't manage the club."

Williams was in Milwaukee this week doing promotion for a beer company . . .

With the Major League Players Association executive board convened in Kaanapali, Hawaii, player representatives voted to drop the "acting" from his title and confirm Don Fehr as executive director. Now he and they, as a group unhappy with the approach of the commissioner and club owners toward a drug program, will come up with their own proposal.

Atlanta's Bruce Benedict said of the union's soon-to-be-announced program, "I think it will shine a different light on the whole thing."

However, Fehr said the program will not deal with the issue of drug testing, thorniest of the drug issues . . .

Phil Niekro, saying his age (46) and career victory total (300) are just numbers, apparently will pitch for the New York Yankees again next season. The knuckleball pitcher said the Yankees have told him they want him back and said he would avoid getting into any type of contract dispute with the club . . .

The Philadelphia Phillies, who told center fielder Garry Maddox, 36, to try his luck in the free agent draft, have re-signed him for one year (probably at about half his previous $675,000 salary) and, to make room, released pitcher Jerry Koosman, 43. But Koosman "has a standing invitation to come to spring training as a nonroster player and try to make the pitching staff." . . .

With the winter meeting getting in gear this weekend in San Diego, a deal is reportedly in the works to bring 300-game winner Tom Seaver, 41, to the Boston Red Sox from the Chicago White Sox.

"We have something we can do with the Red Sox," White Sox executive Ken Harrelson told the Boston Globe, "something on the table." For instance, Seaver, outfielder Rudy Law and a minor leaguer for Al Nipper, Mark Clear and Jackie Gutierrez . . .

As Baseball in Washington Week came to a close, with the major league owners to consider expansion next week on the Coast, the D.C. Baseball Commission surpassed its goal of 15,000 season tickets sold for the team it hopes to land for 1987. The total, a spokesman said, is 15,367, meaning $8,713,089 has been deposited in escrow accounts at area banks.