Lions skipper Danny Shittu headed the only goal of the replay at Ewood Park to secure a Wembley semi-final against Wigan.
Murphy was in Shittu's position of club captain at Rovers until the start of this week, when Scott Dann was officially confirmed as his successor.
After being substituted at half-time during the 3-2 Championship defeat to Peterborough 12 days ago, the 35-year-old former England international has not featured in three subsequent squads despite an injury crisis that leaves Appleton restricted in midfield.
David Bentley joined Lee Williamson and Dickson Etuhu on the sidelines following Sunday's goalless draw at The Den and, in the absence of cup-tied Wigan loanee David Jones, club stalwart David Dunn was thrust into a first start since October alongside Morten Gamst Pedersen in the Rovers engine room.
Central midfielder Jason Lowe played as an emergency right-back due to injuries to Bradley Orr and Adam Henley, and striker Leon Best ended up on the left wing when Marcus Olsson pulled out at half-time with a hamstring problem.
Appleton failed to offer guarantees over Murphy's future earlier this week following a wretched first season at Championship level, and was comfortable with not naming him on a bench that included untried youngsters John O'Sullivan and Anton Forrester.
"If there was one place that we didn't struggle tonight it was in the middle of the park," he said.
"I think Danny, if he's going to be involved with us, he's probably going to have to start the game.
"I don't think he's going to make much of an impact as a substitution. We need to move forward as a football club and we need to look forward.
"You either leave players in your team or out of your team on performance and, from a performance point of view, I picked the team which I thought would try and enable us to get into the next round."