And the Ibrox boss defended his decision to replace Naismith with Kyle Lafferty at half-time, with the Northern Irishman making his first appearance of the season after a hernia operation.
Rangers lost 2-1 on the night in Slovenia and must now hope they can finish the job at Ibrox next week.
Steven Whittaker and Madjid Bougherra both saw red in the Champions League qualifying exit to Malmo and McCoist says he was keen to avoid a repeat.
He said: "It was to keep him on the park. I thought there was a distinct chance that Naismith could have been sent off.
"We did have one or two options but Lafferty has looked good in training and was keen to get back playing. Towards the end of last season he was one of the key players. It's still early for him and he will come good."
Despite the defeat - thanks to an injury-time winner for the home side - McCoist is still confident of booking a place in the group stages.
He said: "I would like to congratulate Maribor on their win although we were very disappointed.
"We felt we were comfortable at half-time. It was an open game and hopefully the second leg will be open too and we can take our chances.
"We created a good number of goalscoring opportunities in the first half. I'm very disappointed but hopeful we've got enough to win the tie and go through at home."
Juan Manuel Ortiz fired Rangers into a first-half lead with his first goal for the club before Agim Ibraimi levelled and substitute Etien Velikinja grabbed an injury time winner.
McCoist added: "It's frustrating but I'm not going to blame individuals - we win and lose as a team. Collectively as a team we weren't as dominant or aggressive in the second half as we were in the first."
On his decision to hand a debut to Carlos Bocanegra, who signed for Rangers on the eve of the game and was granted international clearance just hours before the match, McCoist said: "He is the US captain with 93 caps, he has played in World Cups, he's a good footballer.
"It's not an ideal situation, I agree, but we have been stretched in that centre-half postion and we felt we had to take the chance."
Maribor coach Darko Milanic felt the whole game turned on the decision to replace Naismith, who had been cautioned in the first half.
He said: "The key thing was the change of Naismith for Lafferty - we had space in midfield and a lot of movement after that.
"I was very surprised about the change because it changed the match completely."
Asked if he felt that McCoist had made a mistake, Milanic replied: "That's for you to judge. I'm just saying I thought it changed the game."