It certainly is rough to have two major issues arising at the same time. The last thing you need is to have the rug pulled out from under you job wise when faced with a significant medical issue. That happened to me, and getting back on my feet was rough. At least with your present employer, there is a history of tolerance relative to your medical history. This tolerance may not be present with the prospective employer. Having been in management for almost all of my career, I know what can happen and how it is done. I am hesitant to make any specific recommendations for your situation.
Medical wise, I would definitely get a second opinion since your surgeon has been unable to advise you about possible occurrence of lesions in the small intestine if you were to get an ileostomy. Have you been tested for Crohns? I would want to keep my j pouch if at all possible, but that will undoubtedly require frequent scope and other exams. I have FAP, and regular scope exams have been a necessary part of my life. If it is determined that your j pouch must be removed, there are two surgical options that do not require having an external bag: the K pouch and the BCIR. There is a lot of information for both procedures on the internet. Please feel free to send me a PM with any questions you have.