A couple facts to consider:
1. McDonald has been charged with FELONY domestic violence. Under CA law, domestic violence is a "wobbler" crime that may be charged as either a misdemeanor or a felony depending on the facts of the case (i.e. severity of the domestic violence and extent of physical injury) and the defendant's prior criminal history. Looking at the facts of this case, they elected to charge it as a felony. Even if McDonald managed to plead down to a misdemeanor conviction, he would still be subject to a six-game suspension with a potential escalator because the victim is pregnant.
2. In addition to the victim being pregnant, preliminary reports indicate the victim displayed physical evidence of abuse in the form of bruising. This is a key fact in the event that the victim either refuses to testify or changes her statement, a la Ray Rice's now wife.
The looming question now is whether Harbaugh and the 49ers will hide behind the need for a final adjudication, even if the facts are damning on their face. We know they chose to do this with Aldon Smith, playing him in a game just two days after he slammed his car into a tree with a BAC that was twice the legal limit. And even after Smith pled no contest to that charge and his three illegal weapons possession charges, they still refused to reprimand him with Harbaugh proclaiming that he was still a member of the team in good standing.
The 49ers are currently employing the same avoidance strategy with Chris Culliver, who is awaiting his own felony weapons possession charge after allegedly threatening someone with illegal brass knuckles following a hit and run. There is little doubt that the facts show Culliver is guilty of possessing that weapon, which is a felony in CA.
Whether Culliver and McDonald start in the season opener will speak volumes about how seriously Harbaugh and the 49ers view these offenses. Do they play them for the entire season as the legal process in Santa Clara continues to be delayed? That would hardly be "above reproach."