The O's parted company with manager Geraint Williams following Saturday's 3-1 home defeat by Hartlepool, a result which left them just a point above the relegation zone after a poor run of one win in 11 games.
Assistant manager Kevin Nugent will take charge on a caretaker basis for Monday's game but Thornton will play no part as he begins a two-match suspension for picking up his 10th booking of the season at the weekend.
Jimmy Smith is the most likely candidate to replace Thornton in the starting XI, while striker Scott McGleish should retain his place after recovering from a foot injury in time to play 65 minutes against the Pools.
Captain Stephen Purches, who has missed the last three games with a torn calf, faces a late fitness test.
If Purches fails to make it, on-loan Aston Villa defender Eric Lichaj could deputise.