This is getting into some tricky territory, similar to trancing rabbits— for some rabbits, the acute stress/discomfort may be worth doing a short, necessary procedure, as the alternative is not doing it or it being immensely stressful/anxiety-inducing for the rabbit/dangerous due to flailing.
If your vet was a rabbit-experienced exotic vet (not a dog/cat vet; not an exotic vet with little rabbit experience either; needs to be both rabbit experienced and exotic), I err more on the side that they may be weighing the pros and cons based on handling your rabbit. If the vet was not a rabbit-experienced exotic, I would say it was more likely a well meaning, but maybe not well thought out recommendation.
There are several videos here that show varying techniques to trim nails: https://wabbitwiki.com/wiki/Grooming#Trimming_nails
Perhaps you’ll be able to find one that works.
See rabbit.org/vet-listings for a vet, if you do not have one currently.
The answers provided in this discussion are for general guideline purposes only. The information is not intended to diagnose or treat your pet. Seek the advice of your veterinarian or a qualified behaviorist.