If I understand the situation correctly, it could play out one of two ways.
If he applies for a transfer and petitions the NCAA, they may rule that Harbaugh, et al, ran him off. If so, then he can play his one year immediately. Or, if he does not petition but simply transfers, he has to sit out a year. That is a viable possibility, because he played as a true freshman and therefore as an incoming senior transfer would have 2 to play 1.
Given the questions about his knee and at least two diagnosed concussions, the transfer redshirt year would seem to make sense, regardless of whether he petitions to play immediately and regardless of whether the NCAA actually bothers to rule on it before fall camp begins.
Ultimately, he will need to convince a staff somewhere that he is worth a 2 year scholarship risk.
I think if I were a head coach, I'd want the redshirt year to permit time after the concussions and also to continue the knee rehab. That also gives him time to fit into your defense, so his one playing year can be productive.