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The failures aren't relevant though. they are looking at being dismissed for conduct, not academic, issues. Ending someone's career for calling other sites and leaving a rotation early is a draconian punishment. Even that guy at Case screwed up more times than this before being dismissed.
Any promotion and graduation committee takes into account the whole case, meaning both academic and professional matters. OP has been called in front of them before for failing boards. OP being called in front of them again for a professionalism issue does not mean they will ignore past issues just because they are under the realm of academic. As I alluded to, they could have even had him fail the rotation (which would be justified) and dismiss him from a both academic and/or professional standpoint. They have grounds for both.
Also, you're implying that all he did was call other rotation sites. He called other rotation sites in an attempt to circumvent his own clinical education office's decision. That is a big deal, and may demonstrate a lack of respect for authority. Those sites even felt it necessary to contact his school and inform them of his action. He did not discuss the issue with ClinEd, he did not ask them if it would be alright for him to contact the other sites to see if they had a spot, he just took it upon himself, thinking he could find away to get around their decision without involving them.
These really aren't minor issues. Doing a single one would be cause for action in a job or residency. I personally hope these actions were done out of naivety, in which case I hope his Dean is merciful, but it should be understood that these are not benign actions.