I just watched the game on replay. I agree that selecting Stewie and Morgan for apparent punishment is slightly strange if you just look at their minutes at the beginning of this particular game. When they were pulled (and they were pulled at exactly the same time, so I don't understand how their minutes can be different), UConn was ahead 6-2 and all 6 points had been scored by those two players. Morgan made 2 free throws after being fouled on a drive, and Stewie made two field goals with Morgan assisting on both of them. Morgan had also gotten a rebound and was running the floor as she should.
On the very first possession, Morgan did make a lazy pass to Stewie, and Stewie did not move to the ball. The end result was a turnover. That was the only obvious example of sluggishness on their part.
Geno referred at least twice to the fact that the sluggish start did not only occur today, but in all of the last three games. He said something about the team expecting the games to be easy, which might account for the sluggishness.
So I'm now thinking that this was meant not as a specific message to those two players, but to the team as a whole. He was saying, "If you think these AAC games are easy, then I can certainly make them hard. Let's see how you do without your two best players!" It was also a message to Stewie and Morgan, not exactly about their own play, but about their leadership. "Hey, you are the leaders of this team. If the team is sluggish at the start of three consecutive games, then you have to own that." And also it was a message that a lot of coaches (and bosses) like to deliver on occasion: "You can be replaced." He let the big players know that the team can win without them, so he is not going to be forced to play them just because he needs size on the floor. Maybe he thought that they (including Kiah) were getting a little too comfortable with the fact that their minutes were basically guaranteed.
So the end result is that the other six scholarship players are all fully warmed up for extended minutes on Monday if they are needed -- Nurse / Chong / Williams / KML / Jefferson all got 30+ minutes and Courtney got 17. Presumably they also got confidence that they can play a credible UConn basketball game at both ends of the court, score points, rebound, and defend, without relying on their "big" sisters. So IF foul trouble, sluggishness, or poor shooting is a problem for any of the UConn bigs on Monday, they will get a quick hook and we will see some of what we saw in today's second half. After today, it seems less likely that UConn will lose if they have to play a small lineup for extended minutes against the Gamecocks.
It's even possible that Geno decided that the problem was with everyone EXCEPT Stewie and Morgan. Maybe he thought that in the first five minutes of the Memphis game, the other players were slacking off and were relying on those two to win the game. So he figured they would be fine for Monday, and he wanted to put some stress on everyone else.