A Chris Dagnall brace and a Marlon Harewood effort saw Barnsley advance with Dean Bowditch scoring a consolation for the hosts, who had Alan Smith sent off late on.
But Flitcroft's thoughts after the match were very much centred on the injury to Etuhu, who was stretchered off after a clash of heads with Adam Chicksen.
"I think it threw my players quite emotionally, it can do that to a team," he said.
"It worried me to be honest. When he came past me he wasn't unconscious but he wasn't responding initially.
"MK Dons' staff were impeccable and were very professional in the way they dealt with it. He has gone to hospital for a check but he is okay, he is stable."
Flitcroft said the injury was a bad one and something he will not forget in a hurry.
"You certainly don't want to be involved in anything unsavoury and it certainly was," he said.
"Kelvin is a tough boy and when you see him flat out on the pitch and coming past on a stretcher with blood strewn over his nose and face, it is something that will probably haunt me."
Flitcroft said he had also been informed one of his players had been abused by an MK Dons fan and stepped in to defend his man, with the supporter escorted out of the stadium as a result of other crowd members reporting him to stewards.
"I felt one of the fans was having a go at one of my players so I responded in the heat of the moment, I will protect my players to the hilt," he said.
"I think MK Dons are looking into the incident. I just asked if a gesture had been made could the man be taken out of the stadium."
MK Dons are expected to release a statement in regards to the issue and Flitcroft would not confirm which player was abused, although he did say it could be an "alleged racist incident".
The result puts Barnsley into the quarter-finals of the FA Cup and Flitcroft admitted he had pushed his players hard in the lead up to the match.
"The result meant everything, there has been so much detail and planning over a week now and we have put a lot of effort in," he said.
"I have asked the players to sacrifice seeing their families and we went to see Doncaster against MK Dons, and I'm absolutely delighted with the players. The first half was a masterclass."
MK Dons manager Karl Robinson hit out at referee Michael Jones' decision to send off Smith in injury time.
Robinson said he had seen replays of Smith's aerial challenge with Rory Delap and believes the former Manchester United man's reputation preceded him.
"I didn't even know it was a foul," he said.
"But you see Alan Smith going to try and compete and right away ultimately the referee thinks 'that's Alan Smith, he has tried to do him, sending off'.
"You could see it and, by the way, how quick did he go for his card? It looked like he couldn't wait to do it but if he sticks to his report he will know he has made a big error."
The home side rallied at the start of the second half and Bowditch's goal gave them hope of getting something out of the tie but it was the slow start to the game that riled Robinson.
"I thought in the first half we were poor," he said.
"We were as bad as we have been but the second half was more like us, tried to retain the ball and play the game right.
"It was a very split game, they were the better team in the first half and we were better in the second half."
MK Dons have not won in any competition since beating QPR 4-2 in round four of the FA Cup and Robinson admits being left with just the league to focus on could prove to be a blessing in disguise.
"Whilst we have had a good FA Cup run we've had a bit of a disappointing league campaign," he added.
"Now, in some ways, to focus our minds on one thing might not be a bad thing."