"As it stands now, yes," Harbaugh said.
"Two principles are woven together here. I feel like the way the facts are and what's known, that he has the liberty to play in the game."
McDonald, a starter at defensive tackle, has practiced all week after posting $25,000 bail Sunday afternoon. According to Harbaugh, he has been "fine" in practice, despite missing the first 19 minutes Wednesday and the first 40 minutes Thursday.
No formal charges have been filed against McDonald as the investigation continues. The 49ers, who have stated a zero-tolerance policy toward domestic violence, have cited the need to respect due process. Harbaugh harkened the Fifth Amendment of the Constitution for reporters Wednesday.
49ers general manager Trent Baalke said earlier this week that the team, rather than the league, would handle potential discipline with McDonald.
Still, NFL commissioner Roger Goodell announced last week harsher penalties for league employees guilty of domestic violence -- six games for a first offense and a lifetime ban for a second.
But Goodell said Wednesday at a season kickoff event in Washington that he would act when the time is right.
"I think the first thing you have to do is let the process play out, get the facts and make sure you understand all the circumstances," Goodell said. "We don't [know the facts] right now, and we're obviously following it very closely. But the policy will be applied uniformly across players, coaches, executives, commissioners. I think we made that very clear in the policy."
McDonald also has a DUI on his record from 2010.
McDonald To Play For 49ers Despite Arrest
ESPN 49ers reporter Paul Gutierrez breaks down the 49ers' announcement defensive end Ray McDonald will play in the season opener despite Sunday's arrest.