If it were up to me, I would sit him until it's resolved. SF is just getting started here, and I would hate for the progress he's made get derailed by criticism from the national media (sports and otherwise), the Twitter mob, and the MeToo movement for playing a guy who could very well be convicted of a felony.
I often times wish there was a position in the AD that handled these kinds of things so that it'd be taken out of the coaches hands. Coaches are there to coach. They're not legal experts, counselors and case managers. I think too much responsibility gets put on them in these situations.