Clear the 25th bit of I_CUSTOMCOLOR to disable a track or item's custom color.
Code:
local track = reaper.GetTrack(0, 0)
local color = reaper.GetMediaTrackInfo_Value(track, 'I_CUSTOMCOLOR')
color = color & ~(1<<8*3)
reaper.SetMediaTrackInfo_Value(track, 'I_CUSTOMCOLOR', color)