Relegation-threatened Orient took the lead in the fourtth minute when Chris Dagnall collected a pass from David Mooney to slide the ball past City keeper Frank Fielding.
However, the O’s defence was breached twice before the half-time whistle.
After 12 minutes Freeman powered home a volley which took a deflection on its way into the net.
And the visitors took the lead from a set-piece when Freeman curled in a free-kick from the left and the unmarked Flint ran onto the ball to head home from close range.
Wilbraham settled the issue on the hour when he stabbed home Joe Bryan’s cross from the left for his 16th goal of the season.