Now is the time for him to go. Can’t take the chance with his arm or risk a bad senior year. And you lose negotiating leverage as a senior.
HE was drafted at #861! I believe that he went low based on uncertainty in the health of his arm.
He also does not have overpowering speed, but neither do many successful pitchers. Hell, some guys throwing in the upper 90s become very hittable after you see their fast ball long enough. It's all about keeping hitters off-balance and uncomfortable, and Baker's stuff sneaks up on you.
He has much more value than that. Another good season and he moves up considerably.
His arm has to be the main reason he went so low. And it might be the reason you take the leap now rather than blow it out or be weaker next year. Tough call either way. I’m thinking a pro organization’s training/medical staff would be better for him at this point.