Trufant, who went down late last season, missed the team's run to the Super Bowl, returned to OTAs on Tuesday.
"It's great to get him back," Mallory said. "Even when Desmond was hurt last year, he was in on every single meeting. Even though he was hurt, we didn't lose his leadership. He was there every day. He was out there at practice every day and at the games. It was great just to have his presence."
Trufant signed a six-year, $68.75 million contract extension this off-season.
"But we know that we are getting a healthier body and healthier player back," Mallory said. "It's good to get him back. He adds an awful lot to that room. When he's on the field he adds an awful lot on the field."
"It was kind of a blessing in disguise that other guys stepped up when (Trufant) went down," Mallory said. "If you look at Robert Alford and the level of his play and the level of his game went up. Jalen Collins was able to come in and give us some good and productive play last year."
With the play of Brian Poole at nickel back, the Falcons finally have some depth at cornerback.
"Again, that's helped us in the long run that those guys have that much quality playing time," Mallory said.
Mallory was promoted after spending the first two seasons with the team as a defensive assistant.
He worked with the defensive backs under Marquand Manuel, who was promoted to the defensive coordinator position, last season. In 2015, he worked with the linebackers.
Mallory, the son of former college coach Bill Mallory, coached in the collegiate ranks for 25 years with stops at Indiana, Army, Western Kentucky, Maryland, Oklahoma State, LSU and New Mexico.
Last season, the Falcons started out playing a lot of zone coverage. As the season progressed and the younger players became more comfortable, the played more man-to-man press coverage.
While Mallory plans to continue to stress fundamentals, he believes the Falcons can play more coverages.
"You have to fit what you are seeing offensively, but we feel like we got corners and nickel back that can do both," Mallory said. "They can be effective in zone coverage and be effective in man coverage. You have to be able to play both coverages because I think both coverages are going to complement one another. I think what hurts you in zone coverage you have an opportunity to come back and play man to it and overcome some of those areas that are issues.
"Vice versa, if you are playing a lot of man coverage and other people are going to run some man-beater type concepts that you can come back and play complementary zones against what you are seeing. So, we feel like we've got the personnel to play both. We are going to rep both in practice."
In addition to adding to the depth, the Falcons are counting on strong safety Keanu Neal to grow from his strong rookie season.
"When you look at a guy like Keanu, the position that he plays is probably one of the more difficult positions to play in our system because he's a hybrid between a safety and a linebacker," Mallory said. "There are times when he's down in the box like a linebacker would, but he's got to be athletic enough to match up and cover a tight end. There are times where he has to be able to match up on wide receivers and there are times where, again, he's going to be back playing the middle of the field. So, it is a unique position.
"Keanu, in year one, you saw steady progress throughout the season."