Stewart was shown a straight red card during the 3-0 FA Cup defeat at home to Rotherham on Tuesday night for elbowing Millers striker Alex Revell and he begins a three-match ban.
Fellow centre-half Dean Leacock missed that second-round replay with a hamstring injury and he remains a doubt ahead of Saturday's game.
That means Krystian Pearce could go straight into the starting line-up against the O's following his return from a loan spell at Barnet.
"He enjoyed his stint down there at Barnet, playing lots of games for them - which is exactly what he needed because he wasn't playing here," said Magpies manager Keith Curle.
"We've seen a couple of DVDs of the games he has played in for Barnet. They have been pleased with him and he's done exactly what he needed to do."
Lee Hughes has missed the last two matches through illness and it remains to be seen whether the veteran striker will recover in time for the weekend.