Clint Uttley resigned from his post on Tuesday. He had been head coach of the Redmen since November 2011.
A resignation letter attributed to Uttley said the coach objected to McGill's decision to suspend running back Luis-Andres Guimont-Mota following his arrest last week.
In the letter, Uttley took umbrage with a statement released by McGill on Friday that said "the individual should not have been invited to join our team. That was not in accordance with the values of our community."
He added that he believes in giving people a second chance and noted that McGill did not object to Guimont-Mota's presence on the team when he was sentenced to 90 days in jail time last year after pleading guilty to assaulting a man outside a Quebec City bar.
A source confirmed the contents of the letter to The Canadian Press.
"McGill accepts Coach Uttley's resignation and thanks him for his dedication and service to McGill and the Redmen football team," McGill deputy provost Ollivier Dyens said in a statement. "The University maintains that the pedagogical mission of our institution takes precedence. We wish Mr. Uttley well in his future endeavours.
"As we indicated in a statement last week, we launched an in-depth review of our rules and regulations governing participation in varsity sports to ensure that all rules and regulations are aligned with and reinforce transparent decision-making, accountability and commitment to the values that define the McGill learning environment.
"Our review is continuing."
Guimont-Mota was allowed to serve the sentence on Sundays so it wouldn't interfere with his football career.
He was formally arraigned in Montreal last week on charges of assault and uttering threats. He was immediately released on $300 bail and a host of conditions.
The third-year business management student and starting running back was arrested at a downtown apartment. McGill said the player in question had been immediately suspended as per the university's varsity athletics guidelines.
Guimont-Mota's lawyer said the university was too hasty in suspending his client from the football team and didn't know all the facts of the case. Steve Hanafi says the 22-year-old Guimont-Mota is considering filing a cross-complaint against his estranged wife, the alleged victim in the current case.
Guimont-Mota won the Dan Pronyk Memorial Trophy, given to McGill football's most outstanding offensive player, last season.