You are too focused on the GM position, AA in this instance. Owners or team presidents set visions for franchises and give their GM's mandates. AA's mandate was likely to make the playoffs at all cost, especially being in the last year of his contract and with the president who hired him on his way out.
Team's situation isn't as precarious going forward as you make it out to be. Yes, Shapiro has some work to do, but hey, he does have to do something, doesn't he?
He could decide to put Donaldson on the trade block and get a haul for him, or at least a young 3b, 2 young depth SP and a top SS prospect.
Objectively, AA took over a worse situation.