Cottagers striker Bobby Zamora suffered a broken leg following a challenge by Karl Henry when the two sides met in London last September.
Fulham captain Danny Murphy later caused a storm when he criticised the aggressive approach adopted by some top-flight clubs, with Wolves among those he made specific reference to.
McCarthy revealed earlier this week that Murphy apologised for his comments before the return fixture in April.
Nonetheless, the Yorkshireman was left irked by the reputation his side had gained from the episode, so was delighted to see them overcome their opponents with a flowing performance this afternoon.
"I don't think we started in control of the game, but we grew into it and were comfortable - we got better and better," McCarthy said.
"What is pleasing is that we gained this reputation last year for being a dirty team at Fulham by kicking them off the park, which is just so wrong.
"I really enjoyed watching my team play football against them today and beating them in the right way.
"It is nothing to do with (Fulham boss) Martin Jol or the players - it was just that incident last year really did us a dis-service, so it is pleasing to put that to bed."
Kevin Doyle opened the scoring in the 42nd minute when he collected Matt Jarvis' pass and smashed a shot past Mark Schwarzer.
Jarvis then doubled the hosts' advantage in first-half stoppage time, pouncing after Roger Johnson's header had come back off the woodwork.
The result means Wolves, who triumphed 2-1 at Blackburn last weekend, have recorded back-to-back league wins at the start of a campaign for the first time since the 1998-99 season.
They also temporarily moved to the top of the Barclays Premier League table, until Manchester City's 3-2 win at Bolton later this afternoon, but McCarthy is not paying much attention to the standings at this early stage.
He said: "I'm not really bothered about the league position - we start near the bottom every year alphabetically.
"But it's nice to win two games, back-to-back in the Premier League. It is a really good achievement."
It was a generally dominant display from Wolves, who might have added to their lead against a Fulham side playing their ninth game of the season due to their exploits in the Europa League qualifying rounds.
McCarthy was sure facing Ukrainian outfit Dnipro in the competition only three days earlier would have taken its toll on the Cottagers.
"I think Fulham were at a definite disadvantage having played on Thursday night," McCarthy said. "I can't imagine - it will be a long time before I want to get into the Europa League.
"If we look like getting in through the Fair Play League, I'm going to tackle somebody."
Jol admitted his team's European campaign was not making their lives any easier.
"There is a part of me that thinks we can do well in Europe, and there is another part of me that knows it is probably almost impossible to do well and get to the final as Fulham did two years ago," Jol said.
"Of course, if we start playing all the competitions in England, we could probably do without the Europa League.
"But we are in it, and hopefully we can get through to the group stages. I am happy we are in it."
Zamora missed Sunday afternoon's game after picking up an ankle injury and is a doubt for the second leg of their qualifying play-off against Dnipro on Thursday.
Source: Team Talk
Source: Team Talk