I can speak to my career field with a pretty good degree of authority but Front Office major league baseball decisions.... ehhhh, not so much. Even with that established though, the FO made 100% the right decision in not protecting Baddoo in my opinion.
A team only has the 40 slots that they can protect and that often leaves hard choices to make. However I would think that Baddoo wasn't a hard choice in that he had no track record in MiLB and was buried on the depth chart for the Twins. Was it a gamble? Yes of course it was, but one that I would make 100 out of 100 times and probably so would 90% of the rest of the league.
We also have to look at who took a flyer on him, the Detroit Tigers. The major league roster was seriously depleted of front line talent and their minor system was exhausted. Why wouldn't they take a shot at him, they had absolutely nothing to loose (same with Tyler Wells and Baltimore).