They absolutely cannot let Stewart not sign short of a fully legitimate, career threatening injury (which raises other questions). They already have lost a significant amount of potential future talent due to Coppy gate AND, now that they are playing better, will lose future draft position, plus face a J2 next year where they can sign no one for more than $10,000 THEN get their J2 pool cut in half the year after that.
If Stewart does have some kind of career ending type injury, then that may just be bad luck or potentially someone dropped the ball on the background side of scouting. But short of that, AA better get this thing done.
The Pipeline blurb clearly states that the concerns didn't arise until his POST-DRAFT physical. There's absolutely nothing they could have done that they didn't do. As things stand today, potential draftees aren't required to undergo a pre-draft physical for potential suitors. I'd imagine this will be something that's addressed in the bargaining over the next CBA.
Stewart's curve obviously gives him a high ceiling, but he doesn't come with any guarantees. If he's damaged goods (that may simply be a bump in the road) and is willing to take an offer that the organization is comfortable gambling with, great. If he's not willing to take what will still be life-altering money and understand the reason the organization is being careful, let him gamble on himself and go to school.
I'd imagine I speak for many when saying I'd rather have a healthy #9 pick in 2019 than the next Brady Aiken. There are no "got tos" in this situation. I hope he signs because I like his upside as much as everyone else does, but I'd rather have a healthy lottery ticket next year if he's crazy enough to turn down what the Braves are offering when there's clear evidence something's wrong and he may never get a shot at that money again.