Arcadia University fired its president. For no (publicly given) reason.
In the article/interview here -- http://www.philly.com/philly/blogs/campus_inq/Fired-Arcadia-president-says-he-was-banned-from-campus.html -- you have a textbook case for how to leave graciously, without rancor, without poisoning your reputation, even if your employer did things you find outrageous.
I do not know the complete story; I'm not commenting pro or con about this particular case. Rather, I have two points.
First: Always consider what you have to lose by making a stink. This outgoing president says he was shocked; it came as a surprise; he knows more than he's willing to discuss publicly. But it's a "he said/she said" situation. His employer has done something it feels justified in doing, and wants to keep secret. If the ex-president spills his guts, he may get satisfaction... but he will never work in academia again.
Second: Check out unsolicited, candid employee comments about a working environment before you take a job. In addition to general googling of the company name, here is one source: http://www.glassdoor.com/. And yes, there are a few comments about Niagara University up there. (They are not my comments; I neither endorse nor disavow them.)
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