From a legal standpoint, an employee's status as a founder or owner/shareholder is largely irrelevant. There's no basis for special treatment--in fact, depending on how it's handled, such special treatment would, at a minimum, place the company in a potentially perilous legal situation with future cases.

One of the major ideas behind suspending employees for investigations is to eliminate their ability to influence the investigation. Also, it's a immediate precautionary measure to prevent the behavior from continuing should the complaint be found to be valid. In that sense, it protects the employer by keeping them at a distance in the short-term. They can also point to it in the press and in future legal proceedings (if any) as part of a strategy of showing that they took the complaint seriously from the beginning.

I also have never heard of a founder being put on leave. I wouldn't go quite so far as to say it is an admission that the allegations are true. But it is certainly an admission that they have merit and are not so far from reality as to be easily dismissed. I am pleased that Github is taking this seriously, and very sorry for Julie's experiences. This should never happen to anyone in our industry.