Amazing how people can be so cruel..... I work in the same company for the last 16 years (insurance company in Athens) and although my boss (i'm his secretary) who is the CEO is generally a very tough guy, when he found out about my condition almost two years ago, he was so sweet! Although I have been suffering from Crohns for several years, I guess my condition is pretty mild, because I never missed a day off work because of this. When I don't feel well I just call him and tell him I will be a little bit late, and he always says "take your time".
I also appreciate the fact that he never revealed to anybody else my health problems, and when he found out that the child of another colleague had Crohns, he asked me very politely if it would be OK for me to call the guy and try to comfort him, because he was devistated from his child's diagnosis.
So, working in a possitive environment really helps, and I can't imagine how you are coping everyday. If you were living in Greece, you could sue your boss for "discrimination" but, it would take a long-long time until court made a decision.
My advice is that if you can't handle it anymore, try looking for another job. Stress is a big factor of flares as you know, so you don't have to put yourself in this awful situation.
I wish you all the best, and I'll pray that your working life will get better real soon!