"I am curious whether more experienced folks can lend their thoughts on this question - how do you react to NON-baseball dysfunction or bad behavior at a target school."
Unfortunately it is hard to have this kind of information exposed until a tragedy like this happened at Maryland. It is rare to find social media or other places where kids or families talk about situations like this. And as others noted, football is bit more crazy when it comes to expectations. But make no mistake, physical conditioning is also a huge part of college baseball and players' toughness is going to be tested.
When you do get down to narrowing your list of seriously interested schools, one thing I did is start saving a PDF of the team rosters (old versions of the rosters typically disappear from websites). Then you can start tracking the transfers and disappearing players. While the reported transfer rate is very high for baseball (as high as 40% for D1), seeing how much churn there is in a roster can be telling. I'm not suggesting transfers relate to abusive practices, but that is one way to get an idea of a team's dynamics. You can also look at stats pages to see how many kids got opportunities to play in a season. If a kid is playing but transfers anyway that could be telling that there are other issues.
Then when it gets closer to making a final decision, be sure you do the visit and talk to the coaches about the program and training regimen. The coach should be willing to introduce you to the trainers, show you the facilities, talk about their training program expectations for preseason and during the season and offseason. And then be sure to go to as many games as you can and sit in the stands and listen to the families talk. Tell them you are thinking about going to the school--would they do it over? How does their son like the program and coach. You'd be surprised what you will hear sometimes. And some of the better high school and travel ball coaches also know more about what the coaches' reputations are.
Unfortunately, situations like this still seem to exist way more often than they should. Like everything on your recruiting journey, conducting a lot of due diligence about the school, coaches and trainers is part of the challenge.