"I am shocked," McCartney told AFL.com.au during the Bulldogs' Australia Post Community Camp in the western Victorian town of Hamilton.
"I'm more disappointed, really, because I can just imagine there are so many people out in the wider community that have grown up, like most of us have, loving the game and respecting the people who drive it.
"I think there would be a huge disappointment, but I think it is really important that this gets played out factually and in the context of the law and not too emotively.
"Because I've been fortunate enough to work in AFL football for a long time now, and I can count on one hand the people I've met that I just wasn't sure about their integrity and their motivation.
"So we're talking about a minority. The majority of people in this industry take their jobs so seriously and work so hard to be good for the game and do a good job – that's the disappointing thing.
"But there's a lot to play out I think. I will watch with interest, and you just hope people that you love and respect are never involved in anything like it."
Essendon has been at the centre of the storm since an investigation into the club's sports science methods was announced on Tuesday.
McCartney, who worked at the Bombers as an assistant coach in 2011, hopes the club will not become a scapegoat.
"There's some fantastic people in that footy club," he said.
"I loved the 12 months I had there and built some great relationships with some incredible people, who are good, good men.
"And I think they deserve the opportunity to have things played out fairly and with proper justice and not have it as a witch-hunt.
"There are too many good people in that club for them to be treated the wrong way."
The Bulldogs beefed up their sports science department over the summer by appointing Graham Lowe to the position of high performance manager and also bringing in a new strength and conditioning coach, Andy Barnett.
However, McCartney does not subscribe to the theory that sports science experts are being given too much power over the way clubs are managing their players.
"I haven't encountered any time where one or two people have dictated the program," McCartney said.
"At the three clubs I have worked at, the allocation of more money to the fitness departments emanated from the question: How do we manage our players better?
"So what does management of a player look like? It basically is about creating an environment where players can progress and get as fit and strong as possible to play an incredibly difficult sport.
"It's also about them not getting injuries and not getting to the stage where fatigue stops them performing at their best. That's a very fair situation.
"As a club, you're number one priority are your players – their welfare and their well-being.
"What you'll find, in almost every case, is that the conditioning people, the strength people, the coaching people and the welfare people all sit down together and plan and come up with programs.
"If you have that in place, you rarely get it wrong.
"It's when egos and peoples' ambitions take over the group, that's when you can sometimes get it wrong.
"So I think the disappointment we all feel now will hopefully get dealt with fairly and equitably and we can get on with playing footy.
"Because right now people are probably looking at our industry and saying, 'How many people are in the industry that aren't doing things right?
"But the reality is that the high majority of people work hard and just want to be part of a successful club."
Adam McNicol covers Western Bulldogs news for AFL.com.au. Follow him on Twitter at @AFL_AdamMcNicol
