Marler, 25, was playing for the first time since serving a two-match ban for calling Wales forward Samson Lee a "Gypsy boy" during the Six Nations.
Referee John Lacey did not see the incident during Quins' 30-6 victory.
"It was not a boot, it was nowhere near a boot - it was a shin," said O'Shea.
Citing commissioner Iain Goodall now has 48 hours to determine whether Marler should face a disciplinary hearing for the incident, with any punishment potentially affecting his availability for England's summer tour of Australia.
But Quins director of rugby O'Shea was adamant that no further action should be taken.
"Any test for a citing has to pass the red-card test," said O'Shea. "Should he do it? No. Is it a red card? No.
"It's disappointing to have to talk about it because I thought his scrummaging was excellent. But he is under the microscope.
"Things happen. We never condone it but if that is a red card there's a heck of a lot of things that happen on the pitch that are worse.
"So I'd focus on the positives. I'll have a word with him, but there are things happen on the ground. He got up, he did something, but it wasn't a red card."
Harlequins boss Conor O'Shea has defended Joe Marler after the England prop appeared to kick Grenoble's Arnaud Heguy in the head during Friday's European Challenge Cup semi-final.