Johnson was offered a one-match suspension for making contact with his head to Fremantle tagger Ryan Crowley's face.
If he had a good recent record, Johnson would have escaped with a reprimand.
But he has been suspended for five matches in the past two seasons, so he finds himself facing the prospect of being sidelined for Friday night's clash with North Melbourne at Simonds Stadium.
And if Johnson fights the ban at the Tribunal, he will risk a two-match ban.
"Things that put yourself in a position to get suspended are unacceptable," Scott said shortly after the MRP handed down its findings on Monday.
"I think we've got an obligation to make sure we look at all the detail and all the issues in a bit of depth.
"But the bottom line is, some people have decided that there's enough there to warrant a suspension and we, as a football club and as a coaching ground and a playing group, can't accept it. Steve doesn't accept it.
"We treat all our players as individuals, but there's a base-level of behaviour that applies to everyone, and he's overstepped the mark too often.
"Now there's some chance that it'll go to the Tribunal and he'll get off, but in a lot of ways that's not really the point.
"We're in this position again, and we need to deal with it, and we'll deal with it strongly."
The threat of a two-game suspension means the Cats are likely to accept the offer of a one-match ban for Johnson.
However, they have until Tuesday morning to make the call.
"Given the main decision-makers are at Tom Hafey's funeral, we'll take a little bit of time to digest it," Scott said.
"It's not ideal, but we're a fair way from making a decision about how we approach it."
Scott admitted that Johnson's latest indiscretion is evidence that the Cats' coaches are "not doing a good enough job" of educating him on how to deal with taggers.
However, Scott is adamant that Crowley, who fell to the turf after being nudged by Johnson, exaggerated the contact.
"There's a lot that goes on off the ball, and the player has obviously crumbled a little bit, so that makes it look a little bit worse," Scott said.
"But from our end, and from Steve's end in particular, he can control his behaviour and it is disappointing that we're in this position.
"It really is a series of very minor indiscretions that are adding up to a decent penalty. That's the reality.
"He got elbowed in the throat (by Docker Zac Clarke) and the other bloke gets a reprimand because he hasn't got a bad record."
Scott couldn't help but crack a smile when asked about the free kick paid to Geelong skipper Joel Selwood early in the third quarter of Saturday night's game.
Selwood was running onto the ground when Johnson dragged Crowley into him, yet the umpire then penalised Crowley for an illegal bump.
"You win some, you lose some, and we won one there," Scott said. "That was a strange decision. We even had a chuckle about it in the box.
"They made some mistakes on the night the umpires, as well as the coaches and players, and that was probably one of them."
Twitter: @AFL_AdamMcNicol
