The midfielder was sent off for a scything challenge on Jordi Gomez after only 11 minutes, with the Spaniard then opening the scoring midway through the second half before Hugo Rodallega wrapped up the points with a late second.
It was not the first time this season Henry had been the focus of attention for his tackling, after a number of incidents involving Joey Barton against Newcastle, while it was also his challenge that led to Fulham striker Bobby Zamora breaking his leg.
McCarthy had been staunch in his defence of the 27-year-old before today but he accepted there could be no other outcome this time, although he did make reference both to Henry's reputation and the challenge by Aston Villa's Steve Sidwell last week that left Adlene Guedioura with a broken leg.
"I've no argument at all with the red card," said the Wolves boss. "It's ill-judged, it's mistimed - it's very theatrical. We've a lad at our place with a broken leg for six months from a tackle from a lad who went for the ball.
"It didn't look as theatrical and unfortunately, with Karl being in the press and the media so often recently, it was never going to be any other result."
McCarthy refused to go into what punishment, if any, Henry will face, preferring to leave the matter for another day.
"I'll speak to him," he continued. "But it's not really for immediately after the game when emotions are running high. I think, for the benefit of everybody concerned, it's best kept until Monday."
Wigan boss Roberto Martinez described it as the worst tackle he had seen at the DW Stadium and admitted he feared Gomez had broken his leg.
Martinez said: "It wasn't just the first contact. Karl catches Jordi with his knee, he comes with real force and you fear the worst. I felt it was a broken leg. He was a very fortunate man."
Gomez himself was surprisingly magnanimous about the challenge, saying on Sky Sports 2: "It was a hard tackle but hopefully I'm okay."
Wigan failed to capitalise on their numerical advantage during the first half, although Gomez should have scored just before half-time when he glanced a header wide from Charles N'Zogbia's cross with Marcus Hahnemann beaten.
The Latics were much improved after the break, though, and, after Franco Di Santo had missed a glorious chance within seconds of the restart, Gomez showed him how it should be done with a superb free-kick in the 65th minute.
N'Zogbia was pulled back on the edge of the box by Dave Edwards and Gomez sent his shot into the top corner.
Wigan continued to threaten and they got their second goal - only the fourth they have scored in the league all season - with five minutes left when Rodallega deflected in Christophe Berra's attempted clearance following a through ball from N'Zogbia.
Martinez did not feel the red card helped his side, with memories of their 1-1 draw against Sunderland in similar circumstances still fresh, and he was proud of the way the Latics came through in the second half.
He said: "I didn't want to see that situation happening. The crowd got anxious, you feel that you're going to win without knowing how.
"But the second half was completely different. I was extremely proud of the players, how they found the solutions, how they learned from the last experience against Sunderland, and we created many chances.
"The pleasing aspect was we limited Wolves to nothing. The maturity and responsibility of the players in a no-win situation was very, very good.
"It needed a bit of magic to open the scoring but you could see after the first goal it was going to be a lot easier."