It has been speculated that the point guard could be on his way out to create space on the team's salary cap after a letter to season-ticket holders failed to mention the 30-year-old.
The general manager told ESPN: "Within that letter, I think everyone made a big deal of that because we didn't mention Joe [Johnson] and Deron's name, but I think in doing so, we talked about Brook Lopez and Thaddeus Young, trying to retain them because they were free agents.
"We talked about some of our younger guys because some of those guys we didn't know coming in how successful they'd be coming in the NBA. So I guess we were sort of saying, we know these guys can play in the league, and we weren't trying to slight Deron or Joe. We know what they have, what they bring to the table."
Williams, who averaged 13 points per game last season, is due to earn $21m (£13.6m) during the 2015-16 NBA season.