Sutton, who along with Dave Brailsford helped put the structure in place for Britain to become a cycling superpower, stood down in April after Kenny's team-mate Jess Varnish accused him of making sexist and derogatory remarks.
A British Cycling inquiry upheld the allegations in October after an internal investigation into his conduct.
"Shane never said anything wrong to me personally, he never was out of line," Kenny, who repeated her London 2012 feat by winning team pursuit and omnium gold in Rio, told Reuters at the Revolution Series event in London.
"But to know that it went on in my workplace upsets me because I wouldn't have wanted to have been treated like that and I don't want to see other people treated like that."
Varnish said Sutton had told her to "go and have a baby" after she was dropped from the track team. Sutton was also accused of making derogatory remarks to para-cyclists.
He continues to deny the accusations and is reported to be a target for Cycling Australia.
"He would go out of his way to help me and treated me very well but I can't condone what the investigation proved," Kenny, formerly Trott before marrying track sprinter Jason Kenny in September, said.
She said Sutton's departure had not had any negative impact on British Cycling, which has won 14 Olympic golds in the last two Games, and pointed to the success of a new brigade.
"It wasn't like we had daily contact with Shane," she said. "Obviously Shane and Dave B put the system in place and that is a lot of the reason behind our success.
"But it proved that the system is in place because when he did leave we went and won six golds in Rio.
"Now we know that the girls and guys are coming through the academy. They proved they are ready to step up. At the Glasgow WorldCup they pretty much won every event they were in.
"That just shows that the system is working."
Kenny also welcomed five-times Olympic champion and former Tour de France champion Bradley Wiggins' decision not to retire.
The 36-year-old was surprisingly named on Britain's podium programme for next year.
"The 18 months with him on the team actually took the pressure off because everyone was focussed on Brad and I could just get on with my day to day business," she said.