McCarthy, whose side are 16th, recalled nine players to face the Clarets.
He accepted the verdict, which he called a "deterrent", and said he would not make the same selection move again.
"Everyone else can have an opinion on it [the ruling]. Mine is, I'm absolutely glad it is done and dusted with," said the Wolves manager, whose side are only one point off the relegation zone.
"Will I change 10 players again? I think you will find it isn't possible to do it."
He added: "We'll have to see if anyone else does it but, come on, it's been put there as a deterrent. It has set a precedent and I've accepted it."
McCarthy defended the choice of his side at the time of the match but was much criticised by his club's travelling fans while United were not then in the best of form.
The Premier League's statement on his team selection read: "The Premier League Board has issued Wolverhampton Wanderers FC with a suspended £25,000 fine after deciding that the team fielded in their league fixture against Manchester United on 15 December 2009 was not full strength and therefore in breach of Rule E20.
"The board also deemed that the club had failed to fulfil its obligations to the league and other clubs in the utmost good faith and was therefore in breach of Rule B13.
"The board considered submissions from Wolverhampton Wanderers FC and had sympathy for the explanation submitted by the club in relation to similar cases from previous seasons.
"However, the board ruled that this case could be differentiated from the other matches cited and that disciplinary action was warranted."
The League's E20 rule stipulates that clubs must field a full-strength side in all top-flight games.
However, goalkeeper Marcus Hahnemann was the only name on the Old Trafford team-sheet that had started the victory over Tottenham at White Hart Lane three days earlier.
Former Republic of Ireland manager McCarthy said at the time: "We had a great result at Spurs and every player rated it 9 to 9.5/10 in terms of how hard it was.
This ruling may now lead to a wider discussion regarding the issue of squad rotation Jez Moxey "I need to protect them. If you have another match of that magnitude, you can't cope. We have big games coming."
However, his team selection prompted a furious reaction from some Wolves fans, with many of the 3,000 that travelled to Manchester asking for their money back.
Other observers claimed the selection was unfair to United's title rivals and could set a dangerous precedent.
The Premier League seem intent on ensuring clubs do not field second-string teams in the future.
Their statement continued: "In coming to this decision the board also wants to put clubs on notice that any future rule breach of this nature would be subject to a disciplinary commission that would have available a full range of sanctions."
However, Wolves striker Kevin Doyle, who scored his side's second goal in the win over Burnley, claimed the League's stance was flawed.
"I'm surprised anything has come of it, to be honest," the Republic of Ireland international told BBC Radio 5 live.
"They [the Premier League] are going to have to end up fining a lot of teams over the next few years, I think, if they are going to go about it that way.
Stinks of one rule for the Big Four and one rule for the rest! Panese001 "Are they going to start fining clubs for changing teams in the FA Cup, the League Cup, when they go from Champions League to the league?
"Bigger teams change their sides massively every week, so why is that any different for us?"
The Molineux club's chief executive, Jez Moxey, was more conciliatory and added: "This ruling may now lead to a wider discussion regarding the issue of squad rotation and the Premier League's rules.
"We look forward to fully participating in any such debate at future Premier League meetings."
Moxey, meanwhile, gave his backing to his manager and stated: "One thing that's never been in question is the integrity of Mick McCarthy.
"He picked a team that, in his view, was in the best possible position to get a result in that particular game.
"He made it unselfishly and with the best interests of Wolves in mind."