I am sorry for your loss, and I know you made what you felt was a good decision, but the chances your ball python had IBD are slim to none. In ball pythons it kills very quickly, and almost certainly wasn't "born with it".
I don't think this vet gave you accurate advise at all, and if you decide to get another snake in a year when the chance of IBD infecting a new snake has passed, I most certainly would not be returning to that vet. Any vet worth anything who treats snakes would know that IBD cannot be diagnosed until after the snake has died. They would also know there are MANY things besides IBD that can cause they symptoms you describe.
A good reptile vet would start with asking you about your husbandry, feeding schedule, where the snake was purchased to ascertain the chance of IBD exposure, and a number of other questions to make sure other causes could be ruled out before making a diagnoses of IBD. Especially since any good reptile vet would know IBD is extremely rare in ball pythons, not extremely common.
I do feel sympathy for you, but I still believe a mistake was made and that your snake did not need to die.
Gale