Baker had four charges laid against him following clashes with the Cats' Steven Johnson last Friday night which could have seen him miss up to 12 weeks of football.
The Saints have since chosen to contest two of those charges - risking a 10-week ban if they lose - and while Thompson said that seemed "a lot", he also said the panel's intentions were clear.
"I think the message that they're trying to send is that they don't want Steve Baker's actions to be repeated by any player that plays in the AFL because they were quite severe [on him] and that would be a good thing," Thompson said from Skilled Stadium on Tuesday.
"I don't think we really need to see that sort of thing in footy.
"I don't want to attack Steven Baker, but I just don't think we need to see that sort of stuff in a game of footy. You don't expect to play a game of footy and go out and get harassed off the ball - you just don't need that in your life do you? As a player or a spectator you don't want to see it."
Thompson agreed the umpires on the night could have stepped in earlier to pay a free kick that may have stopped the situation from escalating. He believed the umpiring department would be undertaking a close review of the match, with the lessons learned to be evident next week.
"I think out of the weekend … a player would be quite foolish to do anything like that because you'd probably think the umpires will try to jump in and change that pretty early," he said.
"[And] that's okay because that's what we do as coaches. We sit down every week and work out things that we didn't do too well and try and improve them - umpires are no different.
"Let's be honest they are part of the game, they're making decisions, they actually have to perform every week and they don't get it right all the time. I haven't got a problem with any of that."
Johnson and fellow forward Cam Mooney were also slapped with bans by the panel from the spiteful clash.
The pair will miss three and two matches respectively after the club decided not to contest the charges despite the coach's sympathy for Johnson's situation.
"I spoke to Adrian [Anderson] yesterday and I said that it was a bit hard that Stevie Baker was doing that and Steve Johnson had to accept it," he said.
"But in the end Steven has broken the rules too and we just have to live by that - unfortunately that's what happened.
"We were just a little unsure about how tonight would go if we had contested it so we decided to accept the penalty."
Johnson would have missed at least two weeks in any case after having a broken hand operated on early Sunday morning, but Thompson said the injury had no bearing on the Cats' decision to accept the match review panel’s charges.
