The Giants have long prided themselves on having a “crisis communications” component in their front office.

Over the years, they’ve had to use it. That’s what happens when you find your team in the middle of the biggest scandal to rock modern baseball — the steroid scandal and BALCO. It is required when you work in a city that doesn’t cut sports teams any kind of slack.

So, it wasn’t a surprise that at 7:40 a.m. of the first business day since the shocking video of Larry Baer and his wife Pam having a public altercation surfaced on Friday afternoon, the Giants issued this news:

Team CEO Baer is taking a leave of absence.

“As leaders in the community, we at the Giants hold ourselves to the highest standards and those standards will guide how we consider this matter moving forward,” the statement from the team’s Board of Directors concluded.

Crisis communications has been activated. Yet there are still plenty of questions surrounding the Giants and how the franchise moves forward from this stunning development.

How long will Baer be away? A short time, or permanently? Did Baer, as the statement said, really request “personal time away” or did the ownership group demand it?

Who makes the decisions if there is a big one to be made? Something huge like trading Madison Bumgarner? Who signs off on that? The executive management committee is currently a five-headed body, reporting to a four-headed (without Baer) ownership committee. Those are a lot of people involved to make a big decision.

Who controls the Mission Bay project, which is under way in Lot A and has long been Baer’s pet project?

What happens on April 5, Opening Day at Oracle Park, and how awkward will it be?

Aside from a leave of absence, what else will Baer be doing? Counseling? Community work?

What will the customer reaction be when — and if — Baer eventually returns?

And what does Farhan Zaidi, the team’s president of baseball operations, think about the team he just joined? The man who wooed him to the Giants is for now — and perhaps permanently — away from his job.

Those are a lot of new questions to be swirling around a team already in the midst of transition. The Giants likely will continue to operate smoothly on a day-to-day basis. Most of the people on the executive committees have been in their jobs for decades and are professional and dedicated.

But let’s not pretend this is not a big deal. Baer has been the face of every part of this franchise for 25 years. From bringing in investors to making connections in the community to getting the ballpark built, to personally selling charter seat licenses, to attempting to steer the team through the BALCO steroid crisis, Baer was front and center, with all decisions funneling through him. One of the reasons the departures of former owners Peter Magowan and Bill Neukom weren’t overly disruptive was because Baer was the steady presence with the franchise.

And now he’s not there.

Major League Baseball, according to the Giants’ statement, is “taking the lead in gathering all facts surrounding the situation.” If there are more shoes to drop in this situation, MLB is in charge of finding them.

And there may be. Any investigation should be handled with the same diligence that an incident involving a player would be.

What will the long-term repercussions be? We don’t know.

What we do know is this is one more ugly moment in what has been a very difficult year for the Giants. The team has had to plan far too many funerals. There is concern about filling up the ballpark. About finding a way to win games. The beloved manager is in his final year. The primary owner, Charles Johnson, was involved with embarrassing political donations that rubbed much of the Giants’ customer base the wrong way.

And now the man who was charged with navigating the team through these rocky times is out. For now. And for who knows how long?

It is, indeed, a franchise in crisis. A crisis communications plan might not be enough.

Ann Killion is a San Francisco Chronicle columnist. Email: akillion@sfchronicle.com Twitter: @annkillion