My favorite cat that traveled so well in his crate disappeared and I rescued a cat at the shelter = less than one year old but not really a kitten. She hates the crate and howls I have seen some...
I'm a little disturbed by your vets reaction. While anti-anxiety medications shouldn't be routinely administered and isn't a cure all for these situations, there are valid situations where chemical help is the safest and best way to treat phobias and anxiety during a training period.
This goes for cats as well. The feliway is a very good recommendation. If that does not work, amitriptyline (Elavil) is my next favorite tool.