I agree that it's hard to get good information. You probably won't be able to tell on your interview day. Even people in malignant programs rarely acknowledge what's happening to them--some combination of confirmation bias and stockholm syndrome (and of course the surgeon trainee mentality that equates suffering with learning, which may or may not be reasonable). Trust your gut and all of that, but don't think you'll be able to just ask about it on interview day and get useful information.
The only somewhat useful thing is to do a rotation there. There was a prestigious but notoriously malignant program in a location that I really favored. I rotated there, believing deep down that this conventional wisdom about the program must have been wrong. Turns out, my experience was consistent with what I'd heard and I didn't end up applying to the program at all.
"The beatings will continue until morale improves." - Program Director
As @SouthernSurgeon says, most people are parroting information they heard from people and sometimes from decades ago.
I'd take a different approach. I think that a lot of this is about expectations and fit. Just because you are a rock star medical student and just because you have a reasonable shot at getting into a 'big name' program, doesn't mean that you should go to one. For example, those two programs that SS mentions have a huge rep for being 'malignant' while simultaneously being leaders in the field. They are academic powerhouses, big programs, with big names. They have high expectations of their residents and largely function in a well establish hierarchy model. There are a lot of people that will thrive in that system. Others, not so much. No surgery program is going to be fluffy clouds, rainbows and unicorns, but many, even academic institutions will be less gogogo/high intensity. I honestly believe that the vast majority of programs that are considered 'malignant' fall into this dichotomy.
However, there are some places that are actually bad places to work and are places to stay away from. They tend to not be well advertised or even widely known, but the signs are all there. Red flag: inexplicable attrition. Most surgery programs will lose residents from time to time. It comes with a long, hard and demanding residency. But, if it is happening in every single class, something is up. People may not talk about it, but the signs are often there, how many residents are 'fills' from other programs that started as PGY3s or higher? Are the upper level classes different sizes. (Real example: PGY5 - 6 residents, PGY4 - 3 residents, PGY3 - 5 residents) Some variablity can be accounted for by people doing fellowships or research years, but it can also be from people leaving. More obvious example would be, while you are interviewing, obvious tension between residents or between residents and faculty. I actually heard on the interview trail: "Ya, I hate that bitch." from one resident referring to another seated at the other end of the table.
Every program has its strengths and weaknesses. My program's biggest weakness is the paper chart system. It creates an incredible amount of scutwork for the residents to plough through. So it really bogs down what could actually be a great program; it's really enough to make it malignant.