This does sound rather strange. Chrlorambucil is normally used to treat chronic lymphocytic leukaemia (CLL) and low grade non-Hodgkin lymphoma!
Yet your vet did not mention either of these diseases....
It sounds odd that it should be used (and I have never heard of it being used ) to treat irritable bowel disease!
You didn't miss something that the vet said...?
Now some "chemo" drugs, in different and very low doses, can be used to treat auto-immune diseases. For example, Methotrexate in much lower doses than is used or chemotherapy -can be used to treat diseases such as rheumatoid arthritis. And in such treatments, the side effects are greatly diminished, if many are present at all.
By any chance....is the vet thinking the IBD is auto-immune? And that's the reason for the Chlorambucil?
I am sorry, I am not a vet so can't really advise you as well as you need.
But I can understand your reluctance to dose her with that without knowing the full story, plus her history of slightly paradoxical reactions to a drug such as Prednisone.
I am presuming all her tests and investigations came up "normal" or they didn't discover anything?
There are a couple of options if you are unsure.
1) You could get a second opinion from a completely different vet.
2) You could maybe try to find a Naturopathic /Holistic or Herbal vet. There are many safe herbal treatments which help with IBS and IBD. That includes dogs, not just for humans.
But of course it's wise to know first that you wouldn't just be trying to treat symptoms, while an underlying disease process was going on unaddressed
But I would also suggest having a detailed discussion with your current vet about her treatment and why it is considered necessary, and your concerns.