Unfortunately, whistleblowers/those who see something that needs to change, and speak up are not valued by Most employers (there ARE exceptions)---and any information can be turned against you. I have known people who handle this masterfully, I am not one of them but I am a Voice----it has worked for and against me....
It sounds like a potentially toxic work environment. They may very well give you decent references, or just provide basic time-worked to a future employer---they don't want to look bad, (or may fear "being sued"--an exaggerated fear but I have heard it expressed) Whatever you do DO NOT sign a statement on any new application saying that you waive the right to see/know what your references have said. (I have noticed this on some applications in the past, I never waive that right---it is an invitation to ...well, you get the idea)
I had the interesting experience of working, again, years later in a facility where I had been very outspoken in the past.
I was met by multiple staff telling me how much better they were now, how much more professional they are than when I was there in the past...basically saying "we remember you and want you to know times have changed for the better"---as they had adopted many of the changes I had once proposed.
Unfortunately, the new Director heard and wanted me out, afraid, I guess, I might find something else...
Oddly, even after that, I worked for the same employer again, this time as a contract worker. Go figure.