Robin Hulbert was dismissed after picking up a second yellow card in the second half and Penney admitted he was disappointed to see the midfielder receive his marching orders.
Penney said: "It was a great three points for us. We have ground out a result. You need battlers, leaders and winners out there and that's what we had.
"There was a lot going on off the ball that was missed and it was disappointing to see Robin Hulbert dismissed. He hasn't played much and his over enthusiasm to impress has probably been his downfall.
"Rotherham were a difficult team to break down and it was a battle out there. We got the goal and to be fair we could have had a couple more. But then we went down to 10 men and had to really dig in to get something out of the game."