Khune had not kicked a ball in competitive matches since December 2018 while Akpeyi featured in four of Amakhosi's six matches this season.
According to Middendorp, the decision to bring Khune back into the starting XI was tough because Akpeyi had been doing well for the club.
He said he had a long chat with the Nigeria international who he said understood and respected the technical team's decision to field Khune for the match against Usuthu.
"Daniel Akpeyi played a fantastic five games so far. It was a bit tough for me but the truth is from the 2006/07 season, Itu Khune has been in the team - he's the captain and it was the right time for him to return," Middendorp told the media in Durban.
"We saw him through preparations on how far he was. I had a long chat with Akpeyi as he had a fantastic start. It was tough but he understood it and showed a lot of respect for it," said the German mentor.
Asked if one of Amakhosi's short-term goals is to win the Q1-Innovation which comes with the prizemoney of R1.5 million, Middendorp said: "We have a very clear target. The beginning of the season is a bit unusual if you ended up in position nine, falling out from position eight."
"We work hard to put players in place. We will reach our target. We want to win every game. I'm not thinking about Q1 whatsoever. If it comes it's fine, perfect no problem, we will take it," concluded Middendorp.