Thompson, speaking on Fox Footy's AFL360 program, said the truth will come out when the report is tabled in the coming weeks.
"It's hard to talk about, but from what I know, and I probably know more than a lot of people ... I've read a lot of stuff and know that it's not true," Thompson told Fox Footy on Monday.
"I think the club's made mistakes, we'll admit that when the times come. But as far as drug cheating ... we certainly didn't deliberately go out to do any of that that.
"And why would we? Why would I start doing it now? Why would Doc [Bruce] Reid, after 40 years, start cheating now? It's just crap to think that we would be part of that.
"In the end the truth is going to be told about everything that's happened in this saga. The truth is going to come out because this is too big now to go back."
Thompson said there was still a "fair bit" of truth to come out about the club's supplement regime in 2012, and said the club would be scouring ASADA's report to check its accuracy.
"When the report comes out, we've got to make sure what's in the report is right. There's going to be a fair bit of work done by a lot of people in a short amount of time," he said.
Thompson was lured to the club at the end of 2010 to work alongside new coach Hird in a partnership to restore Essendon as a force, with Evans at the helm.
He said it was "really sad" that Evans had resigned after suffering health issues after Friday night's game against Hawthorn.
But he signalled a new direction for the club under Little after the club was briefed by its new chairman on Monday.
"[He was] really, really positive, [and was] saying that David's done a lot of good work getting us to this point. But unfortunately he can't carry on, and [Little's] up for the job and he's going to fight as hard as he can for us," Thompson said.
"He's been on the inner circle, as far as being one of David's confidantes, and been working with David.
"I think you'll probably see a little bit of a different approach hopefully."
He also lent support to the embattled Hird, who Little said on Monday was the right man to lead the club into the finals.
Thompson said the coach deserved to remain in his position, and said faith had to be placed in people around him.
"As far as I know and the way good football clubs run, the coach doesn't know everything. Yes, he employs someone, he talks about the program, but as far as the management of the program…" Thompson said.
"They're called wingmen. They're called people who you trust that do the job for you and you just expect that it be done. The good coaches at the good clubs have these people around, surrounded by them. Everything is done right…and that's the way it should be organised."
