Kelly - a three-time premiership star at Kardinia Park echoed the calls of football manager Neil Balme and coach Chris Scott, albeit in a softly spoken way, as they disagreed with the sanction handed down to the 2007 Norm Smith medallist.
Johnson was banned for rough conduct on Sydney midfielder Dan Hannebery after bumping the Swans midfielder while the pair were beginning to run towards the next play.
But Kelly said there was nothing untoward about Johnson's action, and expressed his concern that AFL players have too many fluctuating rules to weigh up out on the ground.
"I think these days it is getting harder and harder to be an AFL footballer and especially out on the ground, with so much happening and so many decisions you have got to make in such a short space of time," Kelly said.
"It's getting really, really hard to know what you can and can't do."
Balme said the club only decided not to challenge the Johnson suspension to avoid risking a potential two-match sanction.
"Unfortunately the system puts you in the position where we have to look at it and say, 'can we afford him to miss two weeks by taking the risk for us to be politically correct if you like by challenging it?' So we have to accept that he misses a week," Balme said.
Kelly also confirmed speedster Travis Varcoe was ready to return from a rolled ankle, and he would prove to be Johnson's likely replacement."The defensive side of his (Varcoe's) game is something we have always really valued and is something that is very important going into a final. Scotty's well aware of that and I'm sure they will have a good discussion in match committee," Kelly said.