Scott said as North coach he wasn't complaining about the Geelong star's one-match suspension ahead of his side's clash with the Cats at Simonds Stadium on Friday night.
But Scott said as a footy fan he was not happy that Johnson was suspended for his clash with Crowley because his carryover points from past offences meant he could not accept a reprimand.
"From a footy fan's perspective, I don't like to see the best players rubbed out of the game for innocuous incidents," Scott said.
"I'm sure (Geelong coach Chris Scott) would say [Johnson] didn't need to do it, but the issue of carryover points I think will come up at the end of the year when we review the Tribunal.
"Because I don't think anyone wants to see the best players in the game sitting out for incidents that they probably shouldn't be rubbed out for."
Johnson was charged with level one misconduct after a head clash with Crowley during the second quarter of the Cats' loss on Saturday night.
A player with no Tribunal record would have been offered a reprimand for an early guilty plea, but Johnson's poor recent record meant his penalty was increased to a one-match suspension by 71.78 carryover points and a 30 per cent "existing bad record" loading.
Scott said it was not his job to come up a solution that would improve the Match Review Panel's points-based offence system.
But the Roos coach would prefer that the system was skewed to give players the benefit of the doubt for minor offences.
"We don't want players doing silly things all the time either, but we play a pretty aggressive, confrontational contact sport and sometimes things happen that players should be warned about," Scott said.
"If they're repeat offenders then I suppose that's what carryover points is there for, but I just think that you look at the (Johnson) incident in isolation and I think he shouldn't get a week for that in my view.
"But that's only my opinion.
"It's a hard job (but) I'd prefer to see the things that could go either way go the way of 'Let's get the good players out there playing'."
Chris Scott was less forgiving of Johnson when he spoke about his report on Monday.
"Things that put yourself in a position to get suspended are unacceptable," Scott said shortly after the MRP handed down its findings.
"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."