I didn't get the big deal, either. It didn't make sense to me that B'Elanna would be so upset about being treated. If she is so preoccupied by the past moral habits of her medical practitioners and their techniques, then it seems like she should refuse ALL medical treatment.
I just didn't understand the Captain's decision. B'Elanna made it clear she did not want to be treated by Crell or benefit from any of his discoveries. I don't think Janeway had the right to refuse that request, even if it was made simply as a result of B'Elanna's racism towards Cardassians.