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.