With the NFL season underway, 49ers head coach Jim Harbaugh has displayed hypocrisy by allowing a player to start the season opener just one week after a felony arrest.

The 49ers defensive end Ray McDonald was arrested Aug. 31 in San Jose for suspected felony domestic abuse against his pregnant fiancée.

“I’ll speak for myself, I’ll speak for the 49ers; we’ll not tolerate domestic violence,” Harbaugh said in a radio interview Sept. 2 with KNBR radio. “The second principle is going to be, we’re firm believers in due process.”

But McDonald, who posted a $25,000 bail and was released from Santa Clara County Jail just six hours after booking, was present three days later at practice. He went on to start the season opener Sunday, tallying three tackles as the 49ers defeated the Cowboys 28-17.

Harbaugh is going to have to do better than that. If he is smart, the head coach will reconsider his decision and bench McDonald until the investigation concludes.

So far, Harbaugh’s actions and his mention of due process indicate that the 49ers’ domestic violence policy consists of sitting on its hands waiting for the legal investigation to conclude and the commissioner to take action; a policy that is, at best, no better than that of the other 31 teams in the league.

It is far from zero tolerance.

In a vacuum, or perhaps on any other team, playing McDonald the first week of the season might pass as logical. Some would argue that a head coach’s job is to field the most talented team possible and await a decision from the league before taking action.

But the McDonald situation is different. His case is just the latest of many controversies the 49ers organization has had to face in recent years.

McDonald’s arrest came just three days after the issuing of a nine-game suspension of linebacker Aldon Smith for personal conduct and substance abuse violations.

Smith, the team’s premier pass rusher, has been arrested for two DUIs and a misdemeanor weapons charge since January 2012. Smith also missed five games of the 2013 season while in rehab for alcohol abuse issues.

McDonald marks the 49ers 10th player arrested since 2012. That’s more than any other team in the NFL.

Harbaugh needs to put his foot down.

Letting McDonald start Sunday sent a message—to the media, fans and players—that Harbaugh is not serious about reversing his team’s trend of off-field legal issues.

In fairness, the faith Harbaugh has put in due process does establish the coach’s trust in both the legal system and NFL protocol. No head coach wants to issue a penalty prematurely or without all necessary protocols having been followed.

But Harbaugh is more than just a head coach. Known for his strong personality, Harbaugh is the face of the 49ers from an organizational perspective. He was the first 49ers figure to formally speak to the media in reference to the McDonald case.

If the 49ers’ pattern of off-field issues is expected to change, Harbaugh must use the McDonald situation to institute that change.

Harbaugh’s failure to bench McDonald was a mistake. In the wake of a preseason made infamous by turf issues at the new Levi’s Stadium, a contract holdout by right guard Alex Boone and Smith’s lengthy suspension, the last thing the 49ers needed was another off-field distraction. Although the 49ers won their season opener handily, the impending media backlash and questions of integrity will do nothing but harm the team in the long run.

Harbaugh is not the only one in the hot seat.

McDonald’s arrest came just three days after NFL Commissioner Roger Goodell revised his policy on domestic violence cases, upping the minimum to a six-game suspension for first offenders after suspending Ravens running back Ray Rice in July. Rice was suspended a mere two games after a domestic violence incident involving his then-fiancée.

If Goodell wants his new, harsher domestic violence policy to be taken seriously, he would also be wise to act swiftly in the McDonald case. While there are many different facets of the case to consider, the short window between Rice and McDonalds’ cases adds an element of urgency.

The McDonald case is a crucial one. As the legal investigation proceeds, the decisions made by Harbaugh and Goodell in the coming weeks will become crucial in shaping the procedures followed on player conduct issues for years to come.

The eyes of the NFL will continue to focus on Harbaugh in the McDonald case, a case that the head coach has handled hypocritically as of week one.