Jackson, who is an AFL Players Association board member, also said it would be unfair to question the validity of Watson's 2012 Brownlow Medal.
Watson told Fox Footy's On The Couch on Monday night that he signed a consent form last year that included permission to administer AOD-9604, believing the substance was legal at the time.
Jackson said he hoped all Essendon players would be allowed to play on this season after making a "relatively honest mistake".
He described Watson as a "guy of the utmost integrity and character" and said the midfielder's honesty reflected well on the Bombers.
"They're not trying to hide anything as a player group, they know that what's happened isn't ideal," Jackson said on Tuesday.
"All I can say as a fellow player and an AFLPA board member is that we hope the Essendon playing group are left to play footy and it doesn't impact them too much.
"They were put in a tough position.
"We just don't want to see any good players have their careers affected by what seems like a relatively honest mistake on their behalf."
Jackson said there were more extenuating circumstances for ASADA and the AFL to consider than just the substance administered to the Essendon players.
"Whilst the policies are all about the individual taking responsibility, I think there is a greater issue here and that has to be addressed," he said.
"You've got to remember a lot of these guys are young guys, they're straight out of school.
"Any other 19, 20, 21-year-old wouldn't have the life skills or qualifications to be speaking against people of proper authority in their realm, in this case it's a football club.
"There are senior players in that as well, but it just sounds like the due diligence and the processes in this example weren't quite followed properly and as a consequence the players have suffered."
Watson's Brownlow Medal has already been called into question, but Jackson said he wouldn't have won the AFL's highest individual honour because of any athletic advantages gained from the Bombers' program.
"I think it's very unfair to even raise that as an argument against Jobe and his individual successes last year," he said.
"It doesn't matter how fit and strong you are … you have to be able to play the game, you have to have smarts, you've got to be skilful, durable and yes, you've got to be athletic.
"He's a man of real integrity and character and I'm sure if he thought he was getting an unfair advantage outside the rules that was known to him, he wouldn't have gone down that path."
Nathan Schmook is a reporter for AFL Media. Follow him on Twitter: @AFL_Nathan
