Two days of good news for 49ers

Updated 5:35 pm, Monday, November 10, 2014

The 49ers' season began 10 weeks ago with damage to their image, their roster and their hopes for a calm season.

Within the course of 48 hours, NFL Commissioner Roger Goodell hammered Aldon Smith with a nine-game suspension, and police were called to an early-morning party at Ray McDonald 's house where they arrested him for suspicion of felony domestic violence.

On Monday, the 49ers received a one-two dose of good news. Smith returned from his suspension, as scheduled. And the Santa Clara County district attorney announced there would be no charges filed against McDonald.

Combine that news with the victory over the New Orleans Saints, and the 49ers are in as good shape as they have been during the 2014 season.

Yes, it's loathsome to talk about issues of drunk driving, illegal weapons and domestic violence in the context of what it means for a football team. But that's what the NFL in general, and the 49ers in particular, have been about recently.

Smith did not get his punishment reduced. He has now lost almost an entire season - nine games this year and five last year while he was in an alcohol rehabilitation program - in his young career. One can only hope that he has learned a hard lesson and will change his behavior. The 49ers have gone out of their way to protect and forgive Smith, in hopes that he'll fulfill his promise as one of the great pass rushers of this era. We'll see if their strategy works.

McDonald hasn't missed any time while his case has been under investigation, a development that has brought the 49ers under intense criticism, including from this column. I believed the 49ers should not have played McDonald while he was being investigated for such a serious crime, one that has been ripping apart the NFL this season, and that has long been swept under the rug. I thought they should have designated him inactivate, meaning he would be paid, an opinion shared by many, including former NFL players. The organization appeared tone deaf to the firestorm raging around them. But as the investigation spooled out over not just weeks, but months, it became more and more clear that charges were unlikely.

The decision by the district attorney not to file charges vindicates the decision of Jim Harbaugh - who took a straw poll among reporters to see if they were against 'due process' - and the 49ers' organization's choice to play McDonald. Internally, all were convinced that McDonald was innocent and that the problem was a 'crazy woman.' To make sure everyone knew whom they believed was to blame, there were ongoing leaks to that effect.

But the seven-page district attorney's report paints an ugly scene at McDonald's home that night. We will never really be sure of the details because the 49ers' close ties to local law enforcement compromised the investigation. The district attorney concluded that they would not be able to get a jury conviction - which is what they are looking for when they file charges. Both parties reported that McDonald's pregnant fiancee had struck him first and he had forcibly restrained her. The district attorney's office made a point of noting that failure to file charges does not mean they believe the alleged victim was lying.

The investigation was complicated by a compromised San Jose Police Department. Officer Sean Pritchard, who worked privately for the 49ers, was at the party before the 911-summoned officers arrived. The report indicates that Pritchard was helping McDonald navigate the interests of women who were not his fiancee. The department has instituted new policies to prevent such blatant conflicts of interest.

Also complicating things, according to the report, was a lack of cooperation from McDonald's fiancee and 'the number of potential witnesses, some of whom were not forthcoming with what they saw.' Those eyewitnesses included many of McDonald's 49ers teammates.

'The fact that the appropriate charging decision is clear that does not make it simple or easy,' the district attorney reported. 'Facts surrounding the incident remain unknown despite extensive investigation.'

The 49ers now might believe this is all behind them, though that's not quite true. The team failed to show leadership on the issue, failed to address domestic violence even in general terms, and did not respond to community groups that reached out to them. McDonald may not face charges - and this case is playing out the way so many other domestic violence cases do - but domestic violence remains a serious issue in the NFL. A proactive stance by the 49ers would go a long way toward healing their image. Instead, the owners of the team have been undercover most of the season.

Now, the 49ers will focus on the more mundane issues of getting players such as Patrick Willis and NaVorro Bowman healthy and back on the field. They still have a difficult road ahead of them. Around the same time they were landing back in San Francisco after their flight from New Orleans, the Green Bay Packers were asserting their dominance on 'Sunday Night Football.' The Packers are one of three teams the 49ers are trailing in the race for an NFC wild-card berth.

But, 10 weeks after they were sent reeling, the 49ers are adding bodies and shedding controversies. Just in time for a seven-game playoff push.

Ann Killion is a San Francisco Chronicle staff writer. E-mail: akillion@sfchronicle.com Twitter: @AnnKillion

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