The Ipswich midfielder, who was the derby winner the last time these sides met in Norfolk prior to his controversial cross-border transfer, was subbed 23 minutes into his second half arrival.
Nunez was barracked before and during his arrival on the pitch but was on a yellow card for a barge on Pelle Mattsson – that sparked a minor melee – before he left a calling card on Jose Cordoba.
The Chilean escaped a second caution but was hooked shortly after by McKenna in a bid to keep 11 visiting players on the pitch in a 2-0 victory.
“So we had to protect the team and protect Marcelino in that situation,” said McKenna. “The same as we did, to be fair, with Leif (Davis), (George) Hirst and Anis (Mehmeti) – the boys on yellows – because it was really important to stay with 11 today.
“At that stage, as our crowd would do, they were trying to get people sent off. So it was important to get as many of the yellow cards off the pitch as we could.
“He’s through this one now, he’s tackled it head-on, you could say, and can hopefully have a big part to play now in the run-in.
“Not starting him was partly just from a physical point of view.
“He’s coming back from injury, played a little bit longer than we would have liked the other day with the Azor (Matusiwa) going off (against Birmingham). So we need to protect him with the game schedule that we have because he’s so important to us.
“Of course, we also knew that was going to add extra to the atmosphere and that might not necessarily be something that would help the team.
“He was always going to come on the pitch and have a part in trying to get us the victory though and it obviously got a little bit heated out there and emotions were running high.”