Scouting and and infrastructure are all good with me.
Non-tendering Villar (or cash-dumping him like Jim Johnson) is a terrible move. He is a valuable piece that teams would love at 1 yr/10M if he were a free agent (just like Schoop last year). They should definitely be able to trade him for a 45-level prospect.
If no one is biting, they already have about the lowest payroll in baseball and the financial situation is not so dire that they'd be forced to cut him. They can keep him and try to flip him at the deadline rather than lose him for nothing. But again, they can and should be able to trade him this winter.