Arsenal booked their place in the quarter-finals with Wednesday's win and are due to meet bitter rivals Tottenham in the next round , but it was by no means an impressive collective performance.
Guendouzi set up the Gunners' first-half opener, which Stephan Lichtsteiner converted, before 18-year-old midfielder Emile Smith Rowe netted just after the break.
Young Frenchman Guendouzi was then dismissed for a second booking in the 56th minute after needlessly tugging on Jordan Thompson, and Paudie O'Connor pulled one back soon after.
He then followed Guendouzi in earning a dismissal late on for a cynical foul on Pierre-Emerick Aubameyang.
While Guendouzi's sending off will see him miss Saturday's clash with Liverpool, Emery is not worried.
"That is football. Things can be positive or negative like an injury, a red card, 90 minutes of hard work that don't allow you to play other matches," Emery told reporters. "A red card is like that.
"We have a lot of players looking to play, to help us and take responsibility. His quality for the team, I am going to prepare with other players for the big match.
"He's playing well. He's playing with a spirit – [he's] competitive. The action is... it's an action, he plays that action as a normal moment in the game.
"He is pushing behind the player. He is playing with the spirit I want today and every match.
"We have spoken. It is very important to control, but I don’t think he lost control. The red card is one circumstance."
Petr Cech made his return after a month out with a hamstring injury, but he endured a difficult day and almost gifted Blackpool a goal when he was robbed in his own penalty area, only to be bailed out by the offside flag when Nathan Delfouneso found the net.
But Emery will not abandon his principles with respect to playing out from the back, convinced Cech can do well.
"When you play with the goalkeeper like this it is normal, with the centre-backs to play the ball under pressure back, and I want to give them confidence," he added.
"It's true, after this mistake the supporters also see it, as the ball is played to him to continue to give him and others confidence playing our style, our idea of the game. He has experience. He can do good. We will continue with our ideas."