Hibs were told on Thursday than the former Rangers man would be banned for two games - including this Saturday's Scottish Premiership trip to Kilmarnock - after an appeal against the dismissal was rejected by the Scottish Football Association.
Williams accepts the suspension is the last thing under-pressure Hibs boss Pat Fenlon needs following their nightmare start to the season but the Englishman insists Thomson's reaction was not a sign of an out-of-control dressing room and instead a reflection of a dangerous tackle that left the player badly marked afterwards.
He told Press Association Sport: "Losing Kevin is a big blow. We have got a fantastic squad and have got people who can come in to his position but with the start we have had, he's probably been our stand-out player. His quality has really shown and we are starting to see a fit Kevin Thomson and how he runs the game.
"Whether the manager spoke to him is between the two of them. But I spoke to Kevin at the time on the pitch and he didn't think it was a sending off. He reacted to the tackle but he didn't make any contact with the lad and that's why the club appealed.
"Discipline is important in any game. Maybe now that we are in a position that we really need to get results we need to keep 11 men on the park. But my view is that Kevin has been really unlucky.
"I've seen the marks on his back from the lad's boot. It was obviously a bad tackle. Kevin is not a reactive player at all. He's far from a dirty player. He's calm, cool and collected.
"He just reacted to how bad the tackle was. He just thought he was going to come off in a bad way. In that split second when you think a fellow professional is out to hurt you, you are going to react. Kevin was well within his rights to stick up for himself."
The score draw with United was the first point Hibs have collected following back-to-back league defeats to Motherwell and city rivals Hearts.
But their chances of seeing off Killie were boosted by the Ayrshiremen's own suspension worries, with Kris Boyd banned after an off-the-ball punch aimed at St Mirren skipper Jim Goodwin last week.
However, Williams - who has conceded 12 goals in just five games this season - remains wary of Allan Johnston's side.
"Boyd scored against us last year and he's a quality player," he said. "He will be a big miss for Killie, just as Kevin will be for us.
"He would have been someone we would have had to work on to keep quiet, so it's good that he is suspended. But someone else will come in to his position and we can't work any easier for a clean sheet, which is now crucial for us - a massive step in the right direction."