But Paxson insists the front office has a "really good" relationship with its coach.
"Look, it's not realistic to ask Tom or his staff to be happy about taking a player of Lu's caliber off your team," Paxson said Tuesday. "[General manager] Gar [Forman] and I put ourselves in Tom's shoes a lot. Every day, really. And we know what he's facing. We're not sitting up here saying be happy about it. It's hard. It's difficult.
"But what has to happen within an organization is that when decisions are made, that as a group you have to align together, and you have to move forward. And our focus now has to be on how best to take advantage of what we've just done. That's the challenge -- and Tom's going to be a part of that process with us. That's how this works."
The Bulls traded Deng, their All-Star forward who will be a free agent at the end of the season, to the Cleveland Cavaliers for Bynum, draft picks and salary savings early Tuesday morning.
As expected, the Bulls waived Bynum on Tuesday afternoon, clearing his $12.3 million salary off their books. That will enable the Bulls to get below the luxury-tax threshold, which, combined with not having to pay Deng the balance of his $14.3 million salary, will save the team more than $20 million.
Bynum is expected to clear waivers and become a free agent by the end of the week. Though he was suspended by the Cavs for one game for conduct detrimental to the team and excused from team activities, he is expected to be chased on the open market. The Los Angeles Clippers, Miami Heat and New York Knicks are among the teams expected to consider offering him a landing spot.
Expected to contend for the East title at the beginning of the season, the Bulls are looking to the future after losing Derrick Rose in November to another season-ending knee injury and now trading their two-time All-Star forward.
"I had a chance to voice my opinion," Thibodeau said of his meeting with the front office before the trade was made. "Their job is to make financial decisions, to make player personnel decisions, and things of that nature. Their job is to do that. My job is to coach the guys that are here. That's the way it works."
Asked if he disagreed with the trade when he talked about it with the front office, Thibodeau said, "We discussed it, and I'll leave it at that."
It's uncertain how Rose, who was consulted by the Bulls about the trade and spoke at length with chairman Jerry Reinsdorf on Monday night, feels about the deal.
Thibodeau said the Deng deal, and the events surrounding the Bulls' decision to rebuild their roster, would not impact his relationship with Paxson or Forman, which was reportedly strained over the summer when the team decided not to retain Thibodeau's lead assistant, Ron Adams.